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J. Braz. Chem. Soc., Vol. 26, No. 6, S1-S38, 2015. Printed in Brazil - ©2015 Sociedade Brasileira de Química Supplementary Information 0103 - 5053 $6.00+0.00 SI In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach Juan A. Castillo-Garit,a,b,c Yovani Marrero-Ponce,b,c,d,e Stephen J. Barigye,*,f Ricardo Medina-Marrero,b,g Milagros G. Bernal,b,g José M. G. de la Vega,h Francisco Torrens,c Vicente J. Arán,i Facundo Pérez-Giménez,d Ramón García-Domenechd and Rosa Acevedo-Barriose aCentro de Estudio de Química Aplicada, Facultad de Química-Farmacia, Universidad Central “Marta Abreu” de Las Villas, 54830 Santa Clara, Villa Clara, Cuba bComputer-Aided Molecular “Biosilico” Discovery and Bioinformatic Research International Network (CAMD-BIR International Network), Los Laureles L76MD, Nuevo Bosque, 130015 Cartagena de Indias, Bolivar, Colombia cInstitut Universitari de Ciència Molecular, Universitat de València, Edifici d’Instituts de Paterna, Poligon la Coma s/n, E-46980, Paterna, Spain dUnidad de Investigación de Diseño de Fármacos y Conectividad Molecular, Departamento de Química Física, Facultad de Farmacia, Universitat de València, 46100 València, Spain eGrupo de Investigación en Estudios Químicos y Biológicos, Facultad de Ciencias Básicas, Universidad Tecnológica de Bolívar, 130010 Cartagena de Indias-Bolívar, Colombia fDepartamento de Química, Universidade Federal de Lavras, 3037, 37200-000 Lavras-MG, Brazil gChemical Bioactive Center, Department of Microbiology, Central University of Las Villas, 54830, Santa Clara-Villa Clara, Cuba hDepartamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain iInstituto de Química Médica, CSIC, c/ Juan de la Cierva 3, 28006, Madrid, Spain

Table S1. Random, but not exhaustive, sample of the molecular families of antibacterial agents studied here

*e-mail: [email protected] S2 In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach J. Braz. Chem. Soc.

Table S2. Results of the classification of active compounds in the training sets

Active compounds DP% a Active compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. Mefuralazine 50.55 77.87 Pentisomicin 78.24 71.98 Cryptargol 18.44 –8.10 Betamicin sulfate 88.37 83.59 Arsylen –32.88 –82.20 Argenti fluoresceinas –25.12 –29.86 –51.44 –23.58 Ftalil-medeyol 86.95 82.49 Taurultam 3.39 –23.00 Nidulin 5.56 28.02 Emimycin –36.72 –37.87 Chloramphenicol monocinnamate 55.98 74.62 Mepartricin A 99.59 99.12 84.78 87.40 Azaserine 11.66 24.76 Thiatetracycline 61.92 56.92 Nibroxane –17.37 –2.44 Cefodizine 99.30 99.38 Phosphinothricin –25.52 –7.91 Solupyridine 99.64 98.96 Furidiazina 43.63 69.20 97.35 98.54 Fluoramphenicol 24.29 44.81 Vanyldisulfamide 97.55 92.13 F-8 40.10 59.97 axetil 96.86 95.45 Iodosil-tabl 48.81 33.65 Butampicillin 42.20 49.77 Furaguanidine 30.15 58.34 sodium 91.80 90.11 Protoxyl 13.05 –81.80 Prodigiosin –54.64 –54.58 Sulfanilamide 15.35 –3.11 Annvithrin 12.57 9.45 Bismuth cevitamate –24.17 –25.72 Andrographolide sodium bisulfite 60.92 40.22 Docitrol 23.37 13.04 Etisomicin 78.11 79.47 Parabortine 21.67 45.96 Micronomicin 75.10 56.46 Allicin –83.43 –43.61 Nitrocefin 92.37 97.93 Diamide –15.16 –49.56 Cefoxazole 85.10 90.67 Cupri gluconas –2.21 –7.20 Sodium diphenicillin 23.37 29.21 Desderman –12.29 9.67 Demecloxycline 70.85 68.26 Dibromsalicylamide –17.09 –5.16 Furampicillin 57.25 63.99 Demethylthiolutin –49.64 31.05 Fumoxicillin sodium 70.30 76.27 Nifuraldezone 49.78 70.07 sodium 39.73 42.99 Sulcimid 44.53 36.47 Sancycline 48.01 33.01 Nihydrazone –0.11 34.81 Demecycline 62.10 51.13 Planomycin 11.50 13.49 BL-S339 95.65 96.32 Sulfamerazine 56.01 59.24 Palmatine –52.94 –83.05 Sulfathiourea 70.06 56.08 Lenampicillin hydrochloride 85.15 83.71 Sulfacarbamide 63.87 50.84 Aristoplomb 99.78 99.47 Mafenide 12.14 –9.72 sodium 99.12 98.17 Aldanil 61.65 62.69 Sarmoxicillin 67.34 59.75 Mesulfamide sodium 90.78 75.80 84.82 82.10 Sulfaguanidina 63.81 54.33 Aspoxicillin 93.83 91.95 Nifurthiazole 50.61 71.29 52.44 48.66 Nitrofurantoin 50.70 70.61 Bluensomycin 99.09 98.15 Furazolidone 22.09 48.47 Hidroxystreptomycin 99.42 98.93 Sulfathiadiazole 82.10 57.10 Netilmicin sulfate 76.59 68.35 Nifuradene 24.10 52.03 Apramycin 95.16 93.06 Methylacetopyronone –48.73 –48.88 Butirosin 95.57 94.40 Fumigatin –58.01 –64.59 Dihydrodesoxyestreptomycin 98.64 97.55 Spinulosin –41.41 –48.95 acetate 92.63 81.98 Sulfacetamide 41.58 28.49 Propikacin 96.59 95.71 Glycylsulfanilamide 55.92 33.20 Lavendamycin 42.15 60.02 Nidroxyzone 43.98 65.55 Actamycin 77.60 80.64 Sulfaperin 59.01 55.49 Talmetoprim 47.12 22.70 Pentizidone sodium –40.33 –33.22 sodium 98.45 97.53 Septosil 91.34 78.95 Meclocycline 70.85 68.38 Sulfamethoxydiazine 65.29 58.14 Cetocycline hydrochloride 32.41 43.36 Vol. 26, No. 6, 2015 Castillo-Garit et al. S3

Table S2. Results of the classification of active compounds in the training sets (cont.)

Active compounds DP% a Active compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. Rifabutin 95.54 94.15 Timoxicillin sodium 88.79 91.58 Broxyquinoline –83.23 1.58 Fenbenicillin potassium 41.29 46.96 Clioquinol –97.01 –2.66 cresyl sodium 73.44 78.38 Chloroxine –63.76 –31.84 Forbisen –16.75 –13.73 Diiodohydroxyquinoline –24.38 –23.66 Furbenicillin 91.32 90.92 Korinal –52.09 –17.08 93.88 94.50 Nitroxoline –38.90 –17.25 97.95 98.53 Binoxol –76.43 –77.31 Bromtetracycline 77.93 72.63 Bactofuril 40.65 62.80 Tetracycline 63.23 52.71 Furacril 14.74 60.60 Doxycycline 62.10 50.86 Furalazine 23.08 68.35 Oxytetracycline 73.92 66.53 Captan 30.14 49.10 Dithyral –32.72 –18.97 Phenolsufazole 88.49 51.88 Metioxate hydrochloride 36.01 16.59 Melarsenoxyd 31.78 39.53 W 1889 19.02 23.51 Sulfathiazole 66.72 55.46 hydrochloride 77.14 72.29 Furazoliumchloride 16.76 41.35 sodium 99.74 99.68 Furmethoxadone 23.86 52.32 Penethacilline 33.66 32.79 Aureothricin –56.14 10.67 Pleuromulin –38.70 –40.17 Sulfametrole 67.64 83.23 UTH 31 –56.92 –61.94 Nifurimide 25.63 55.00 Amikacin sulfate 98.18 97.72 Melarsen 84.32 59.18 Butikacin 96.62 95.81 Showdomycin 5.40 3.66 Carfecillin sodium 63.75 64.71 Minimycin 31.28 23.37 Propampicillin 57.25 63.99 Sulgin ASG 77.25 67.86 Sulfamazone sodium 99.35 98.67 Anticapsin –32.92 –33.06 Clomocycline 78.71 73.32 Sulfalene 65.02 57.80 Sulfoxyl-salvarsan 73.07 83.34 Dimethylhomosulfamin 3.94 –31.79 Cefaclomezine 89.03 81.65 Chlorozotocin 60.87 75.69 sodium 94.35 93.48 Negamycin 30.33 13.56 Vaneprim 94.32 85.02 Thiocarbarsone 75.92 23.39 Domigon 54.62 28.34 Chlorquinaldol –64.96 –36.23 Framycetin 98.69 98.44 Tilbroquinol –66.85 –54.29 Neomycin C 98.69 98.44 Tiodonium chloride –23.33 –42.53 hydrochloride 75.77 76.16 Dipyrithione –6.52 48.22 Pirbenicillin sodium 90.01 91.69 Akritoin 50.70 70.60 Galactosulfonum 96.91 96.14 Sulfachlorpyridazine 69.67 66.58 PANS 61.32 47.43 Sulfaclozine sodium 60.27 61.75 Glucosulfone 99.99 99.96 Lavulino-INH –8.88 5.49 Stearylsulfamide 41.58 28.56 Rifordin 93.83 92.54 sodium 98.82 99.40 Miran 17.55 55.48 Fuzlocillin 97.44 97.83 Sulfiodizole 74.67 77.54 sodium 99.30 99.46 Mequidox –27.63 –44.03 Formo-sulfamerazine 99.58 99.54 Dioxidine –9.86 –29.12 Glycinemethyltetracycline 89.10 80.63 Sulfamidomaleyl 73.73 57.74 98.94 98.38 Amifenozin –15.13 –8.59 Methymycin 15.37 –9.39 Sulfadiazine 47.44 61.75 Neomethymycin 13.54 –11.78 Butarsen –62.85 –77.00 Capreomycin 1A 99.95 99.89 Sulfamoxole 61.55 54.77 Cuprimycin 98.59 92.78 Methylsulfathiazole 64.15 59.28 sodium 63.75 64.71 Sulfamethoxazole 52.74 56.19 Fibracillin 81.37 86.06 Sulfasuccinamide 73.73 56.75 Khinoin –1.47 –16.15 Soluseptamid 80.35 65.07 Plauracin 72.25 73.62 S4 In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach J. Braz. Chem. Soc.

Table S2. Results of the classification of active compounds in the training sets (cont.)

Active compounds DP% a Active compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. Sulfaethidole 80.80 68.91 Mupirosin 39.21 29.52 Sulfatrozole 68.64 87.42 Kanchanomycin 60.23 55.05 Nifurdazil 37.07 61.09 Disulformin 99.98 99.91 Sch 29482 19.35 30.85 Piroxicillin sodium 99.87 99.85 Cordycepin 23.41 46.14 Rolitetracycline 69.98 55.84 Sulfatroxazole 52.74 56.02 Morphocyclin 76.65 61.15 Sulfafurazole 56.12 42.36 Chloramphenicol palmitate 55.98 74.55 Alfasol 97.25 94.33 Steffimycin 79.72 58.86 Nifurethazone 38.55 43.98 Streptomycin B 99.88 99.77 Bismuti camsilas 6.95 –14.42 sodium 99.78 99.61 Linatine 38.74 40.28 Prolinomethyltetracycline 88.57 81.55 Cloxiquine acetate –71.26 –43.21 Virginiamycin M1 72.00 70.86 Nifurpyrimidine 4.84 49.11 E 702 99.84 99.92 Nitrofurfurylideneisoniazid 19.07 57.26 Superciclin ‘farmabion’ 81.55 77.87 Sulfatriazine 86.06 77.40 Meglucycline 95.85 92.94 Plumbagin –67.85 –64.40 Pipacycline 83.47 71.74 Nifurvidine –0.15 45.13 Guamecycline hydrochloride 97.70 95.32 Nitrosulfapyridine 61.22 72.43 Amicetin 96.03 92.84 Carbadox 65.53 65.31 Chloramphenicol stearate 55.98 74.55 Nifurmazole 61.66 76.60 Lividomycin 99.69 99.61 Sulfapyridine 36.62 34.77 Luteoskyrin 82.79 87.63 Pyridinin 36.89 40.14 Aklavin 66.79 39.35 Tiogin 58.77 64.93 Apicycline 94.19 89.70 Tevenel 82.40 76.81 Sulfacholazine 85.40 82.48 Sulfadicramide 45.84 12.01 Chloramphenicol stearoylglycolate 80.45 87.62 Sulfathylpyrazole 55.51 38.51 Fusidic acid –11.60 –13.03 m-Methoxythioacetazone 28.61 12.32 Repromicin 33.12 6.08 Thiethazone 38.22 31.03 Terephtyl 99.20 99.31 11.49 19.87 Thymolated silver sulfone 71.98 86.13 Reseptyl 35.23 52.41 Globomycin 95.49 91.15 Nifurzide 69.10 91.49 Interazin 12.42 62.01 Miloxacin 18.01 20.68 Fumigacin 43.36 34.76 Nifuroxazide 21.74 55.27 Aurenin 65.80 68.23 Ciadox 47.73 41.55 Trypan Blue 100.00 100.00 Agropiren –91.19 –90.20 Tetronomycin 16.06 –1.74 Bemural 64.05 62.73 Lasalocid 25.03 28.91 Corps 62 –19.81 37.86 Rosamicin propionate 72.40 45.88 Nifurpirinol –28.61 9.65 Clindamycin palmitate 51.05 40.46 Medeyol 49.39 43.33 Chlorobiocin 92.88 92.37 Furonazide –36.26 –27.06 Tetramycin 91.92 90.69 Sulfabenz 16.10 6.65 J2 96.57 94.83 Dapsone 13.75 13.11 Oleandomycin 78.46 52.88 Nalidixic acid –32.44 –22.41 Lucimycin 91.58 90.27 Temodox 55.19 31.54 Rifamycin 81.65 78.66 Sulfabromomethazine 73.87 77.78 Cinodine hydrochloride 99.99 99.96 Sulfaclomide 66.18 74.94 Erythromycin 87.12 72.41 Olaquindox 21.89 –3.93 Nogalamycin 95.55 77.36 Homosulfapyridine 33.75 29.42 Davercin 93.61 82.40 Acetylsulfisomezole 70.36 73.82 Nonactin 82.73 78.31 Disulfanilamide 91.99 83.86 Kitasamysin 91.49 78.74 Pyridine 'N' 94.11 89.92 Erythromycin estolate 92.63 81.98 Gluconiazide 43.62 55.81 Troleandomycin 95.94 86.62 Vol. 26, No. 6, 2015 Castillo-Garit et al. S5

Table S2. Results of the classification of active compounds in the training sets (cont.)

Active compounds DP% a Active compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. Sulfamidochrysoidine 69.20 71.34 Midecamycin 94.99 87.53 Nifurizone 64.87 72.22 Diproleandomycin 92.57 80.68 Sulfadimidine 57.12 60.65 Ionomycin 42.94 44.86 Sulfisomidine 56.37 60.58 Aspartocin 99.98 99.99 Thiosuccinazone 57.09 52.75 Carbomycin 96.90 90.84 Sulfacitine 74.99 68.51 Virginiamycin S1 98.97 98.56 Sulfametomidine 67.48 60.87 Rifaximin 93.56 93.02 CS 61 74.18 61.35 Tolypomycin 97.77 96.61 Sulfadimethoxine 76.91 61.16 Rifamide 95.00 92.54 Sulfadoxine 74.00 58.08 Rifampicin 95.70 93.85 68.38 60.19 Foromacidin A 95.44 80.23 Factumycin 80.17 67.10 Antibioticum 6613 99.53 98.86 sodium glucuronate 59.93 68.17 Maridomycin 98.04 94.44 Acrotiazol 99.94 99.72 Lonomycin A 85.82 54.39 Sulfaguanole 86.21 82.75 Plauracin D 98.16 95.91 Sigumid 89.50 76.41 Mikamycin B 99.24 98.28 Peracetin –55.57 –57.17 Diacetylmidecamycin 98.43 95.05 33.60 37.65 Losamycin propionate 97.07 92.74 Glucose-INH 34.38 47.54 Bactocidin –17.06 –27.28 Nifurpipone 27.88 42.87 Relomycin 96.42 86.63 Sulfabenamide 53.25 41.61 Amphotericin B 98.36 98.11 Glucosylsulfanilamide 80.91 70.60 Alboricin 78.91 79.55 Dirithromycin 91.96 71.18 S.U.P. 36 100.00 100.00 Sulfoglycin 53.31 39.02 E1 100.00 99.99 Sulfazecin 98.47 95.22 Coumamycin 99.95 99.92 Rokitamycin 95.18 86.42 Polymyxin B1 100.00 99.99 Neamine 57.36 57.49 Olivomycin A 99.92 99.81 Lenigron –14.61 34.85 Gramicidin 99.94 99.88 Anabial –29.58 9.48 Avilamycin A 100.00 99.98 Clobromsalan –31.13 –10.95 Ditetracycline 99.71 99.19 Joflucarban –12.87 10.13 Flurithromycin 90.07 78.85 Arilid –43.22 –17.34 Rifamazin 88.68 85.90 Triclocarban –21.87 13.80 Pyrrolomycin A –32.58 15.89 Sodium nifurstyrenate –18.54 8.48 (3S,4S)-3-Ammonio-4- 89.95 81.69 [(carbamoyloxy)methyl]-2- oxoazetidine-1-sulfonate DJ 6783 –13.46 –1.65 Mesalazine –48.63 –44.19 Myxin 33.06 2.31 Alahopcin 54.74 56.00 Nitrozide 24.60 39.62 Florfenicol 63.42 54.24 Benzalide –56.49 –41.06 Texazone –8.48 –12.90 Acroteben –39.52 –19.01 Salicylazobenzoic acid 14.84 34.25 Flavoteben –39.52 –18.97 Cefivitril 95.05 97.44 Protozide –19.33 4.70 96.19 97.20 Diphenizin –1.23 26.20 Cefedrolor 76.07 77.46 Sulfoniazide 63.88 62.75 sodium 98.04 98.70 Salazosulfamide 78.47 77.21 Ciprofloxacin hydrochloride –4.22 –1.43 Maleylsulfathiazole 91.11 87.55 AM-833 11.81 –0.51 Sulfabenzamide 41.58 29.58 Gloximonan 94.75 95.00 Nitrofen –28.69 3.73 97.41 97.68 Metrasil 71.76 65.53 BMY-28142 92.46 90.12 Cinoquidox 31.03 13.14 L-640 876 88.20 92.66 Nitrofurathiazide 89.95 93.69 Quatrimycin 63.23 52.71 S6 In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach J. Braz. Chem. Soc.

Table S2. Results of the classification of active compounds in the training sets (cont.)

Active compounds DP% a Active compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. 97.43 98.86 Saphenamycin 15.13 31.21 Amidapsone 61.89 55.06 Chlorocardicin 93.57 95.04 SC-28538 48.94 59.04 Cefuroxime pivoxetil 97.72 95.49 Succinylsulfathiazole 91.11 87.20 S825 455 31.50 44.77 sodium 75.45 75.21 ICI 176910 76.88 72.20 Ceftizoxine sodium 89.23 90.63 U-56407 57.55 59.51 Sulfo-mesarca 66.42 55.84 Terramycin X 56.92 48.21 Neoarsphenamine 0.47 35.75 Acidophilin 98.99 98.23 Benzylsulfamide 11.28 –10.85 Actinobolin 34.59 33.88 Urea stibamine 93.53 4.18 Actinomycin D 99.99 99.95 Formylsulfamethin 69.42 69.17 Actinonin 28.82 27.23 Acesulfamethoxypyridazine 79.03 77.11 Aklavinone 1 27.40 17.00 Sulfacetenum 78.70 74.94 Amicetin 96.23 92.85 Antimycin –35.48 –34.08 Amikacin 98.18 97.72 Brodimoprin 10.29 5.70 M 62.32 63.22 Cetofenicol –1.19 10.53 7-(5-amino-5-carboxypentamido)-3- 80.96 77.89 methyithiomethyl-3-cephem-4-carboxy acid Chloramphenicol glycinate 70.00 82.56 Cephemimycin 96.31 92.52 Acetylsulfafurazole 70.12 73.82 7-(5-amino-5-carboxyvaleramido)-7- 93.12 88.11 methoxycephalosporanic acid Nifurtoline 67.80 78.18 7-(5-amino-5-carboxyvaleramido)- 94.99 88.24 3-(methoxycinnamoyloxymethyl)-7- methoxy-3-cephem-4-carboxilic Imicillin 88.25 94.06 Aminochlorthenoxycycline 68.44 53.05 Diaveridine –19.27 –27.35 5’’-amino-5’’-deoxybutirosin 97.53 96.94 Furaltadone 49.32 65.05 1-N-(S-4-amino-2-hydroxybutyril)3’4’- 96.30 95.40 dideoxykanamycin B 94.61 81.19 1-N-(S-amino-2-hydroxybutyryl)- 98.34 97.90 kanamycin B PAS-glucoside 41.26 41.86 1-N-(S-4-amino-2-hydroxybutyryl)- 99.93 99.89 lividomycin A Sulfasymazine 71.55 77.03 5’’-Amino-3’,4’,5’’-trideoxybutirosin A 94.51 93.34 Astreonam 99.18 98.97 810 A1 99.82 99.24 PS-5 18.14 21.68 Antibiotic 890 A1 36.87 40.63 37.08 45.48 Antibiotic A-2315 71.18 69.96 Actinobolin 34.59 33.88 Antibiotic A-16316-C 94.24 88.56 Glucosulfamide 99.14 97.69 Antibiotic A 16886 I 81.18 70.86 Nifuroquine 50.86 61.31 Antibiotic A-26771-A –36.47 17.59 Citromycetin 7.08 11.04 Antibiotic A-26771-B 21.57 11.23 Acidum benzamidosalicylicum –25.40 –23.64 Antibiotic A-26771-C –68.26 80.72 Piperazide –24.47 –11.59 Antibiotic A-26771-E 7.75 –19.39 Casperon –12.11 4.19 Antibiotic A-32390 A 50.42 46.38 Flumequine –39.70 –33.21 Antibiotic B-5050-A 96.32 89.39 Tioxacin 25.88 13.04 Antibiotic B-5050-B 96.32 89.39 Droxacin sodium –37.32 –36.86 Antibiotic B-5050-F 96.63 90.36 Larusan –38.53 –18.57 Antibiotic BL-S786 96.12 96.77 Orthovanizide –24.89 –19.15 Antibiotic BU-1709-E1 96.99 96.29 Sulfanitran 77.38 81.37 Antibiotic C-43-219 95.99 95.89 Nifuralide 67.68 83.57 Antibiotic C-2801X 96.91 95.20 Acediasulfone sodium 54.79 47.33 Antibiotic CP 35587 69.06 86.05 Sulfavanilum 46.33 17.76 Antibiotic DE-3936 85.82 54.39 Quinoxidine 72.35 51.18 Antibiotic FR-29038 79.87 77.30 Vol. 26, No. 6, 2015 Castillo-Garit et al. S7

Table S2. Results of the classification of active compounds in the training sets (cont.)

Active compounds DP% a Active compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. Thiozamin 76.23 72.72 Antibiotic G-52 75.10 58.23 97.66 99.00 Antibiotic G2201-C –56.60 –54.19 Acetyldisulfanilamide 95.27 89.25 Antibiotic G7063-2 –5.11 –3.62 88.20 94.70 Antibiotic LL-AC541 96.57 94.21 Proethyl 27.45 20.14 Antibiotic LL-BM408 87.21 89.02 Asparenomycin 57.77 71.26 Antibiotic M-4365 G1 32.51 8.50 Etoxazene –37.32 –9.24 Antibiotic M-4365 G2 47.93 24.13 Acidum piromidicum 9.16 24.39 Antibiotic MSD 890 A2 39.66 48.15 Dimethyldisulfanilamide 90.62 75.49 Antibiotic P-2563 2 77.90 72.69 Sulfacecole 76.29 73.30 Antibiotic RIT D-2214 86.99 84.78 Pipemidic acid 27.77 37.80 Antibiotic SC-28762 92.03 70.77 Thiamphenicol glycinate 87.75 81.75 Antibiotic SC-28763 88.02 70.51 Carpetimycin A 60.20 74.26 Antibiotic Sch 14342 89.57 88.55 Ormetoprin –19.27 –27.32 Antibiotic SF-837-A2 92.15 79.92 Metioprim –2.74 –13.97 Antibiotic SF-837-A3 95.56 86.98 Trimethoprim –3.14 –26.86 Antibiotic SF-837-A4 95.56 86.98 Dimerasol 96.69 94.80 Antibiotic SKF-59962 94.84 97.13 Butazopyridine 8.47 47.58 Antibiotic SL 7810 99.88 99.85 Cicliomenol –73.43 –68.91 Antibiotic TL-119 98.21 97.29 Amonal –43.37 –22.91 Antibiotic U-11,921 33.71 26.10 Anisomycin –43.41 –55.65 Antibiotic U-21,699 13.09 2.32 Penicillin I 23.37 28.44 Antibiotic X-206 86.60 86.57 Flavacin 23.37 28.21 Antibiotic X-5108 90.32 83.59 SQ 27327 96.39 98.31 Aspergillic acid –56.29 –42.32 NF 167 57.63 72.71 Bacilysin 28.33 18.47 Spectinomycin 32.63 6.85 23.37 28.85 Kasugamycin 82.49 81.63 Bicyclomycin 52.88 46.77 Mebroxine furoate –30.32 –16.18 Borrelidin 16.52 16.28 Lomondomycin 24.38 30.55 Bruneomycin 73.32 75.98 Phenyl-sedasprin –20.57 –19.43 Cairomycin B 2.86 –2.28 Chloramphenicol sodium succinate 81.80 89.05 3-carboxy-2-quinoxalinylpenicillin acid 83.14 89.59 Phennin –46.76 –48.88 Carfecillin 63.75 64.80 55.83 66.64 60.47 67.66 Sulfacinnamine 11.52 –6.56 P1 27.95 26.58 Malazin 91.77 88.80 Chlorobiocin 86.32 88.08 Dolamina 82.55 77.97 Chlorothricin 97.76 96.78 Phenyl-aspriodine –12.75 –13.46 –11.93 –12.88 Albonoursin –43.11 –41.88 Clindamycin 24.80 13.42 Ticarcillin disodium 73.55 78.15 99.96 99.91 Enoxacin 18.82 25.24 Coriolin B –24.62 –22.93 FCE 20054 81.26 82.40 Cycloheptamycin 99.71 98.79 Arsant 99.25 97.56 Dactylarin –31.04 –49.14 Everninocin 26.76 33.38 4"-O-Deacetyldeltamycin 94.48 85.35 Noprylsulfamide 96.15 97.55 9-Dehydrodemycarosyl platenomycin 75.58 45.15 Aditoprime 1.81 –38.15 Deltamycin A1 96.90 90.82 11.75 20.18 Deltamycin A3 96.90 90.83 46.64 50.53 5-Deoxybutirosamine 42.14 42.14 Sporaricin B 14.51 –13.42 Dermostatin A 65.80 67.78 Cryptolepine –80.45 –78.22 Dermostatin B 65.80 67.78 Salazosulfathiazole 92.85 93.82 3’,4’-Dideoxybutirosin B 93.95 92.68 Kalafungin –14.57 –12.97 3’,4’-Dideoxyribostamycin 77.16 75.83 Ipsalazide disodium 57.55 66.01 5-Dihydrocoriolin C –6.76 3.05 S8 In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach J. Braz. Chem. Soc.

Table S2. Results of the classification of active compounds in the training sets (cont.)

Active compounds DP% a Active compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. Azoseptyl-K 88.60 92.50 10,11-Dihydropicromycin 38.01 13.87 Phthalylsulfacetamide 84.33 76.20 Doricin 99.05 97.80 Sulfaclorazole 66.18 75.09 Echinomycin 99.97 99.94 Acidum sulfaloxicum 93.62 87.19 Elaiomycin –18.61 –43.22 71.66 74.79 Enterocin 61.42 50.60 Sulfapyrazole 56.37 60.63 Enteromycin 34.72 7.07 Nifurquinazol 31.32 63.53 7 beta-8 beta-Epoxyisororidin E 33.74 23.57 Cefuroxime sodium 91.03 90.37 Erythromycin B 80.61 59.54 44.03 49.21 Erythromycin B 9-(o-methylloxime) 90.55 71.75 sodium 88.92 84.24 Esperine 98.05 96.65 73.66 84.81 Eulicin 78.52 67.58 Matamycin 90.35 91.81 Everninomycin C 100.00 99.98 sodium 95.72 95.67 Ezomycin C1 99.95 99.94 Ceftioxide 97.43 98.05 Fluopsin B –93.92 82.48 Norfloxacin hydrochloride –5.85 –5.98 Fluoropolyoxin M 98.86 98.13 Sulfaproxyline 56.74 47.50 Fortimicin A 69.41 52.02 Benzylpenicillin 23.37 28.85 Fortimycin B 25.20 5.51 Tifencillin 39.88 50.57 Gentamicin A1 87.90 82.64 Penicillin V 39.73 42.33 Gentamicin A3 88.98 84.17 disodium 81.37 78.85 Gentamicin B 88.37 83.59 92.43 89.40 Gentamicin B1 88.72 84.83 44.04 49.29 Glycinothricin 95.62 92.10 61.14 67.14 Griseolutein A 25.44 19.56 56.24 48.78 Griseorixin 52.64 40.20 Suncillin sodium 95.85 93.04 Griseusin B 67.52 65.61 45.35 50.96 Halomicin A 93.02 90.68 Cephalosporin C 89.95 87.70 Halomicin C 93.27 91.16 Tetroxoprim 3.70 26.96 Hibrimycin A1 99.24 99.06 Ceprochin –66.58 –79.56 Hydroxynybomycin 0.90 –14.01 Penicillin K 23.37 27.93 Illudin M –70.04 –65.76 Yodiftiol 97.48 96.75 Indanylcarbenicillin 63.75 64.71 Phthalylsulfathiazole 91.11 87.81 Isotentoxine 13.31 –17.94 Rosoxacin –36.29 –26.61 Juvenimicin A2 32.51 8.56 Phthalylsulfamethizole 91.39 88.28 Kalafungin –14.57 –12.97 Balsalazide disodium 57.55 65.71 5-Ketocoriolin B –20.66 –20.76 Griseofulvin –17.80 –44.91 Laidlomycin 81.55 79.16 MDL 19592 69.77 69.57 Lasalocid B 25.03 28.82 sodium 79.26 83.30 Lasalocid C 25.03 28.99 Cefuracetime 84.75 83.75 Lonomycin 69.59 28.76 99.65 99.67 Maridomycin 1 96.37 90.30 Clometocillin potassium 60.34 67.39 Maridomycin 2 97.92 93.89 disodium 63.89 64.46 Megalomycin A 95.43 87.41 Sparsophenicol 79.74 85.49 Megalomycin B 97.44 92.15 sodium 39.48 42.59 Megalomycin C1 98.57 95.12 Penicillin P 39.73 42.34 Mikamycin B 99.24 98.28 potassium 41.29 46.13 Mutamicin 1 84.97 80.22 Meticillin sodium 51.20 29.76 Mutamicin 1a 91.93 91.29 Methylenebis-sulfacetamide 98.21 95.83 Mutamicin 1b 86.50 86.13 Cefsumide 95.24 92.08 Mutamicin 2 69.01 60.54 Azotomycin 94.05 98.30 Mutamicin 2a 82.95 75.91 Pirlimycin hydrochloride 31.61 33.13 Nafcillin 39.73 42.99 Sporaricin A 57.33 35.78 Nanaomycin A –12.50 –11.46 Vol. 26, No. 6, 2015 Castillo-Garit et al. S9

Table S2. Results of the classification of active compounds in the training sets (cont.)

Active compounds DP% a Active compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. Astromicin sulfate 69.41 52.02 Nanaomycin C –9.61 –8.04 Isoconazole nitrate –31.46 18.85 Narbomycin 17.62 –9.22 Cefazedon sodium 97.22 98.60 Neamine 57.36 57.49 Salazodine 93.38 94.46 Neomycin B 98.69 98.44 Quinacillin 83.67 88.83 Neotelomycin 100.00 100.00 Usnic acid 10.55 17.81 Nocardamin 95.20 94.97 Soluarsphenamine 43.13 39.32 Nocardicin G 59.04 61.37 Cefaloram 60.45 58.11 Norplicacetin 85.76 82.10 91.36 95.85 Novenamine 72.10 63.59 97.05 94.42 Oleficin 60.98 50.46 sodium 99.47 99.50 5-Phenylphenoxymethylpenicillin 41.10 44.41 Deoxyfrenolicin –12.50 –11.44 Phlebianorkauranol –56.90 –51.19 Thiocillin 51.06 60.90 Plicatin 72.92 62.67 Ofloxacin 8.23 –2.69 Virginiamycin S3 99.31 99.06 potassium 41.29 46.23 Vulgamycin 63.69 54.48 98.33 98.64 Polymyxin E 100.00 99.99 Congocidine 94.60 89.28 Porfiromycin 52.56 23.20 Lactosylsulfanilamide 97.14 94.90 3-o-Propionyl-5-o-mycaminosyl 62.72 26.91 platenolide 2 Albocyclin –58.80 –67.24 Psicofuranine 57.95 72.21 Clindamycin phosphate 76.92 85.13 Puromycin 78.58 71.09 Lincomycin 32.25 13.83 Pyridindolol –44.66 –31.51 Kanamycin sulfate 92.67 92.03 Quinomycin A 99.98 99.95 Tobramycin 90.12 89.30 Racenomycin A 98.26 97.17 Bekanamycin 93.32 92.65 Rancinamycin 1a –21.99 –20.46 Phthalylsulfapyridazine 91.77 89.04 Rancinamycin 1b –21.99 –20.49 Sodium 74.23 88.83 Rhodirubin A 96.49 92.33 Cefaloridine 60.47 67.66 Rhodirubin B 94.78 88.65 Salazosulfadimidine 91.41 94.32 Rifamycin SV 88.68 85.96 sodium 65.30 82.71 Rifamycin W 80.43 81.89 Prazocillin 75.55 89.26 Rifamycin X 94.42 92.51 Cefamandole nafate 94.96 96.33 Sagamicin 78.84 57.00 Atranorin 30.14 13.21 Salinomycin 72.10 72.57 Cefaparole 95.26 96.50 Seldomycin factor 2 42.14 42.64 60.59 55.42 Sirodesmin A 68.17 90.75 Xenysalate hydrochloride –59.56 –62.40 Steffimycin B 78.39 43.98 44.85 52.77 Spiramycin 1 91.95 69.73 Oxetacillin 60.75 68.12 Staphylomycin S 98.54 98.48 Epiroprim 5.95 29.06 Streptolydigin 73.01 64.70 Farbucillin 73.36 73.93 Streptozotocin 51.61 57.28 Trichothecin –40.67 –42.34 Thermorubin A 41.20 20.09 Cefathiamidine 90.66 89.49 Thiamphenicol 29.27 56.13 Amonal –43.37 –22.91 Toyocamycin 44.20 63.73 Undecillin 23.37 27.93 Tubercidin 18.92 40.85 Mirincamycin hydrochloride 31.61 33.18 Triostin C 99.94 99.97 Viomycin 99.94 99.91 aClassification of compounds by both models, equation (1) [non-Stoc.] and equation (2) [Stoc.]: DP% = [P(active) – P(inactive)] × 100; where P(active) is the probability that the equations classify a compound as active. Conversely, P(inactive) is the probability that the models classify a compound as inactive. This value (DP%) takes positive values when P(active) > P(inactive) and negative otherwise. Therefore, when DP% is positive (negative) the compound was classified as antibacterial (non-antibacterial). S10 In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach J. Braz. Chem. Soc.

Table S3. Results of the classification of compounds in the test set

Inactive compounds DP% a Inactive compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. –85.42 –83.39 Dimepheptanol –83.36 –88.14 Ro 09-179 –21.23 –43.86 Dimethylthiambutane –76.25 –75.38 DCF. BW 683c –77.09 –62.14 Butorfanol –72.89 –68.72 Radicinin –35.69 –33.04 Etonitazene –10.79 20.35 3-Episiostatin B –7.38 –15.40 Hydroxypethidine –60.60 –69.84 Thiacetazone 12.98 12.20 Ketobemidone –73.34 –77.15 C3-DHCeA –43.83 –22.85 Levomethadylacetate –72.86 –80.00 BL-1743 –68.82 –69.05 Levorphanol –82.26 –83.82 Dimepranol –83.85 –89.30 Meptazinol –82.78 –85.15 LK-274 –21.12 –28.88 Tenalidine tartrate –73.39 –79.52 Ethoxene –82.86 –82.07 Antallan –27.24 –28.37 Ketoxal –60.29 –60.62 Febensamin –84.87 –90.19 Citenazone 9.16 24.17 Dioxoprometazine hydrochloride –4.34 –32.08 AIDU 50.82 48.89 Difenilhidramine hidrocloride –84.99 –90.62 Oxolin –50.65 –48.88 –74.32 –82.38 Xenygloxal –18.17 –14.08 hydrochloride –70.53 –68.73 BVDU 38.76 38.38 Cycliramine maleate –77.63 –77.86 Arildone –49.65 –51.64 Clorfenoxamine hydrochloride –79.30 –83.61 TSKI- VI 97.19 96.63 hydrochloride –84.47 –90.15 Indinavir 41.67 45.87 Meflopenhidramine hydrochloride –80.02 –86.79 Zalcitabine –6.02 –3.95 Metildipenhidramine –84.99 –90.62 Brometenamine –3.32 –49.15 Ciclizine hydrochloride –84.40 –87.34 Cloral betaine –33.78 –28.06 Ametobenzepine –84.99 –90.62 Calcii bromoaminoacetas –35.91 –47.38 2-Propanol, 1-(dimethylamino)-3- –77.45 –84.76 [phenyl(phenylmethyl)amino]- Trichlorourethan 1.45 –4.87 hydrochloride –88.95 –92.75 Isopral –52.30 –43.59 Histamithizine –78.60 –73.51 Thiourethane –54.94 –65.83 –83.44 –85.64 Etiron –59.21 –63.85 Pimetixene –81.06 –75.91 Bromobutanol 24.64 –23.88 Tripolidine hydrochloride –82.63 –79.08 Aleudrin “Beckmann’’ –44.86 –38.52 Etiloxamine hydrochloride –83.50 –83.67 Vernelan –24.61 –30.99 Borimamide –24.53 –54.74 Agr 449 –68.36 –70.13 Hiproheptine hydrochloride –86.50 –85.22 Sedanfactor solucion –65.61 –67.78 Nigrifactin –86.44 –84.40 Cloretate 60.97 60.85 Histapipendine hydrochloride –83.44 –83.04 Alcabrol –63.11 –60.95 Azatidine maleate –83.14 –83.63 Nitroinosite 99.80 99.99 Tironamine –69.75 –64.96 Cetohexazine –66.49 –59.22 Trazitiline –83.93 –86.79 ferriscorbone 6.14 2.16 –77.97 –71.37 Bason –76.92 –72.38 hydrochloride –82.26 –81.14 –12.83 –18.56 Acidum etidronicum 31.20 70.89 Carbromide –59.99 –57.82 Colestipol –70.45 –75.28 Baldrianol –38.55 –46.43 Oxiniacic acid –29.58 –39.89 Calcii diethylacetas –77.01 –77.18 Nicomethanol –82.10 –77.73 –72.37 –72.88 Mepiroxol –56.39 –62.20 Hedonal –61.80 –66.33 Meglutol –37.35 –37.32 Aponal –60.64 –64.63 Tizoprolic acid –66.61 –59.22 Nevanide –63.71 –61.12 Mapyroxal 3.51 43.67 –82.69 –76.34 glycerophosphate 27.42 –14.11 Mepentamate –60.64 –63.87 Natrii fenbutyras –77.01 –76.67 Ectylurea –38.55 –45.49 Fenbutyramidum –75.79 –74.93 Aminoglutethimide –42.40 –41.16 Clofibrate –59.34 –52.03 Carbavin –60.64 –63.89 Penferon –66.32 –65.64 Vol. 26, No. 6, 2015 Castillo-Garit et al. S11

Table S3. Results of the classification of compounds in the test set (cont.)

Inactive compounds DP% a Inactive compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. –45.37 –57.74 Ciprofibrate –37.27 –23.70 Valproic acid –77.01 –77.12 Xantifibrate 42.66 6.06 LU 2443 –18.45 –36.13 Refortan –27.07 –4.76 Chlorphenacemide –26.17 –23.55 Gemcadiol –82.41 –82.65 –38.55 –45.22 Urefibrate 32.44 44.20 Atrolactamide –64.65 –62.68 Fenofibric acid –41.54 –29.22 Tetharbital –19.03 –37.88 Treloxinate –32.39 –26.70 IL-16 –23.71 –18.71 Dulofibrate –45.25 –22.35 Brofoxine –39.15 –37.39 Clofenapic acid –56.71 –47.28 Beclamide –72.27 –68.99 Nicofibrate hydrochloride –45.32 –29.39 Buramate –53.50 –62.00 Clofibride –24.56 –40.47 Mephebarbital –13.42 –21.81 Itanoxone –54.95 –46.47 –65.13 –71.42 Ciproximide –50.96 –42.31 Zebromal –46.64 –42.68 –72.13 –69.21 Athotoin –44.05 –46.59 Chlorotepine –69.65 –63.35 Nirvanol –39.29 –42.62 –53.53 –46.21 –38.55 –45.28 Pecajine –74.83 –73.03 Tetrantoin –39.29 –42.30 Dicarbine –82.14 –84.77 –13.42 –21.78 Cintramide –46.23 –73.83 –65.13 –71.42 Roxoperone –23.78 –37.11 Phenythilone –48.98 –43.79 Meprotixol –67.34 –78.83 Metetoin –44.05 –55.28 Tetrabenazine mecilate –66.29 –79.22 –47.42 –52.69 Metoxepin –69.19 –80.22 hydrochloride –69.99 –62.54 Docloxytepin succinate –45.29 –20.09 Hexetal –13.42 –23.48 Flucindale –70.07 –76.33 Ferroglycine sulfate –65.61 –68.18 Rolipram –58.37 –67.05 Ferro-drops –67.35 –67.90 –77.16 –76.37 Ferrosi fumaras –46.39 –49.54 Diclorpromazine –58.50 –47.79 Iron aspartate –24.61 –30.99 –34.80 –23.43 Orotonsan Fe 10.28 1.57 LM 08050 –36.92 –54.73 Ferrocholinate –83.38 –92.53 Flutizenal 12.61 14.44 Feramid –66.25 –59.52 SCH 23390 –76.46 –73.80 Ferrosi ascorbas –20.63 –20.77 Timelatem maleate –68.26 –51.21 Fructosum Ferricum –77.05 28.36 Eticlopride –34.10 –30.01 Ferrogluconat –2.21 –7.20 –32.00 –23.33 Glucofer –50.96 82.53 Penflunidol –32.72 –25.99 Calcium sodium ferriclate 90.66 99.97 Meperidide –49.22 –50.74 Diciferron –85.01 –68.17 Diopirone fumarate –4.01 3.83 Ferrosi glucoheptonas 17.93 12.95 Flurtaline –65.06 –57.82 Ferrotrenine –54.07 –51.28 Alpentine –15.29 –48.10 Erythrophyll 59.54 95.52 Fluspirilone –36.53 –36.36 Phenolphthalein –52.18 –47.61 Valerylperazine –51.68 –52.21 Aloe-emodin –48.67 –40.31 Haloperide –38.15 –30.53 Aloin 19.78 29.67 Oxaflumazine disuccinate 6.92 1.13 Bisacodyl –28.81 –23.36 N-Hydroxymethyl-N-methylurea –43.19 –66.95 Danthron –54.01 –47.66 Perhydro-1,2,4-thiadiazine 1,1-dioxide 3.39 –23.00 Emodin –36.46 –26.88 5-fluorocitosicine –27.46 –24.21 Phenolphthalol –72.11 –67.44 Bis(ethylmercury) sulfide –85.23 –90.20 Butanolum –87.50 –86.94 Bis(O-ethylthiophosphono) disulfide –83.54 95.02 Sango-stop –5.74 –23.80 Pentachlorophenol –48.41 10.76 Adrenalone –58.66 –63.72 2,4,5-Trichlorophenol –68.78 –40.59 A-peest 12.70 13.00 2-Chloro-4-nitrophenol –51.04 –11.74 S12 In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach J. Braz. Chem. Soc.

Table S3. Results of the classification of compounds in the test set (cont.)

Inactive compounds DP% a Inactive compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. Naftazone –23.82 –17.90 Chloromethyl 5-nitro-2-furylketone –32.85 4.26 Hydrastinine hydrochloride –65.03 –72.88 2-Nitro-5-(2-nitrovinyl)furan –12.57 41.12 Styptol –54.56 –72.71 1,2-Dibromo-1,3,4,5,6- –8.18 40.73 pentachlorocyclohexane Lodal –75.37 –88.82 Chloro(2 hydroxiphenyl)mercury –81.71 –84.55 Esculamine –5.73 –9.43 4-Nitrophenol –61.75 –36.86 Oxamarin –34.02 –43.26 Methyl 5-nitro-2-furfuryl ether –52.23 –43.43 Besunide 49.27 32.23 O,O-Dimethyl-1-acetoxy 39.08 47.44 2,2,2-trichloromethanephosphonate Morfafen –32.50 –13.41 Bis(dimethylthiocarbamoyl) disulfide –42.93 –37.00 Pytamine hydrochloride –78.00 –83.66 4-Bromophenyl isothiocyanate –50.19 –46.37 MJ 8592-1 –67.98 –58.72 (2Hydroxypropyl)trimethylammonium –82.80 –91.81 hydroxide Hydroxindasate –38.62 –48.17 3,5-Dibromosalicylaldehide –47.17 –36.86 Canrenone –65.14 –64.78 3,4,5,6-Tetrabromo-o-cresol –12.29 9.67 Spiroxasone –50.99 –49.46 6-Chloro-1,2-benzisothiazolidin-3-one –69.88 –34.04 Spironolactone –22.51 –22.38 6-Hydroxy-2-oxobenzoxathiole –40.49 –41.26 Natrii dehydrocholas –27.75 –30.04 3,5-Dibromosalicylic amide –17.09 –5.16 Decinin –28.33 –50.25 2,4,6-Tribromo-3-methylphenol –39.85 –23.28 Lemidosul 1.13 –17.74 4-Chlorobenzoic acid –69.77 –62.54 Urea –59.02 –66.07 1-Hydroxy-4,6-dimethylpirididone –70.73 –63.06 Glycuril –68.36 –70.53 5-(3-Chloropropyl)-4-methylthiazole –72.31 –60.88 Guanamine –27.17 –1.20 5-(3-Iodopropargyloxy)-2- –49.47 –40.89 (methylthio)pyrimidine Melamine 4.35 29.94 3-Acetyl-6-methyl-2H-pyran-2,4(3H)- –48.73 –48.88 dione Glycerol –74.69 –76.08 Phosphorothioic acid –69.69 –4.90 Succinic acid –46.39 –50.97 5-Phenyl-3-(trichloromethyl)thio- 54.21 69.60 1,3,4-oxadioxol-2(3H)-one Trometamol –61.52 –66.57 Trichloroethene –75.78 –59.87 Oxaden 2.63 19.15 Trimethylsulfonium hydroxide –87.67 –93.08 Hydracarbazine –11.91 10.36 1-Pirazolecarboxamidine –48.58 –34.52 -merodrin –35.61 –57.29 Carbamimidotioic acid 18.28 18.05 Merbiurelidin 20.94 –15.49 4-(2-Aminoethyl) –67.92 –64.00 Theobromine –2.67 –25.35 1H(piridotiazin-one) –51.33 –38.53 Mateina –8.42 –39.83 Thiosalicylic acid –61.46 –60.80 DS-1 –81.64 –76.22 2-Hydroxybenzamine –64.65 –61.67 Oradon –39.22 –53.48 2-Methoxynitrophenol –50.59 –36.81 Pallirad –41.87 –50.42 5-Amino-1-phenyl-1H-tetrazole –31.26 8.74 Cystamine –83.42 –42.37 Salicylic acid dihydrogen phosphate –4.97 30.78 Amifostine –33.25 18.90 1-Phenylsemicarbazide –46.75 –45.77 Ficusin –67.61 –66.25 N,N,2-Trimethyl-1,3-dioxolan-4- –78.11 –86.69 ylmethylamine Beroxan –57.72 –65.96 Acetanilide –76.16 –74.86 Peucedanin –56.46 –64.48 3-Hydroxyacetanilide –65.15 –62.18 Batilol –76.40 –78.22 4-Hydroxyacetanilide –65.15 –62.10 Glicondamide 85.07 65.80 N-Phenylacetohydrazide –67.52 –63,24 Methyl palmiroxate –71.47 –79.35 O-Acetyl-5-bromosalicylic acid –20.35 –19.26 Gliamilide 90.48 79.74 O-Acetylsalicylamide –44.26 –44.97 Glisindamide 90.75 83.00 o-(Carbamoyl)phenoxyacetic acid –28.28 –32.33 BPC-151 10.19 22.35 N-Methylacetanilide –78.48 –81.20 Etomoxir –49.14 –45.75 p-Methoxyacetanilide –68.39 –74.63 Vol. 26, No. 6, 2015 Castillo-Garit et al. S13

Table S3. Results of the classification of compounds in the test set (cont.)

Inactive compounds DP% a Inactive compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. TA-078 –53.18 –69.57 4-Hydroxypropionanilide –65.15 –62.37 Palmoxiric acid –68.49 –69.62 Ethyl p-aminobenzoate –66.01 –65.89 Meglitinide –19.07 –26.23 4,5,6,7-Tetrahydro-2-methyl-3- –71.75 –75.22 methylamino-2H-indazole Calcii mesoxalas –25.16 –31.08 Triazino(5,6)quinoline –60.02 –26.18 Tonyol –9.52 –15.96 7-Chloro-3,3-dihydro-2H,9H- –49.70 –28.13 isoxazolobenzoxacin Tiforminhydrochloride –17.11 –27.61 2,3 dihydro-9H-isoxazolo(3,2b) –55.25 –40.90 quinazolin-9-one Amformin –13.57 –23.03 Hadacidin –42.17 –41.26 Etoformin hydrochloride –17.61 –25.24 Carbetimer –62.11 –64.78 PIDH –53.54 –32.23 Fluoxyplin –63.25 –47.74 Benfosformin 53.66 68.56 BA 1 –43.10 –41.18 Mebenformin –19.19 –36.56 Cystogon –61.32 –80.23 Centpiperalone –29.65 –30.97 Fluorembichin –82.96 –84.41 41.96 19.50 Mitoguazone 58.05 45.03 Anisilbutamide 54.48 19.99 Etretin –69.47 –76.34 Anticoman 9.78 –6.47 Pyrimazid –23.68 2.51 Clomoxir sodium –59.19 –52.83 Tetramin –82.86 –82.07 Glycyclamide 43.30 24.25 Caracemide 22.26 –9.03 62.36 49.33 Mitobronitol –20.90 –16.62 53.85 40.07 Chloromethylsilatrane –72.12 –14.32 Scyan –68.41 –70.85 Dinitolmide –16.12 38.25 Enalaprilat 20.20 14.24 Etimidin –43.55 –20.87 Ag 307 18.28 18.05 Imifos –56.65 –17.57 Iodocholine –78.19 –89.45 Spiroplatin –78.93 –79.17 Nitricholine perchlorate –51.60 –64.74 Tegafun –13.65 –17.32 Disotat-amp –86.50 –85.31 Azapicyl –31.81 –21.20 Guancidine –36.27 –34.21 Leucenol –11.71 –8.18 acetate –20.36 12.55 Uramustine –0.80 8.78 hydrochloride –10.64 26.60 Basidalin –49.88 –49.45 Hydralazine –59.38 –40.56 Imidazol mustan 28.47 60.95 hydrochloride –32.56 –17.57 Asperlin –34.70 –38.03 Dihydralazine –22.15 2.28 Novembitol –84.15 –81.39 Pildralazine –27.70 –16.15 Pipobroman –9.59 –10.80 Oxdralazine dihydrochloride –10.17 8.59 Nifuron –9.98 43.16 MK-534 –34.63 –18.88 Benzotef –27.44 7.54 hydrochloride –42.61 –20.76 Razoxan 26.12 17.17 hydrochloride –9.19 10.05 Dihydroxyacetone –72.79 –73.40 Olmidine –36.79 –36.88 Cyclamic acid 14.86 –13.90 Guanclofine –17.71 –1.35 Melizame –13.65 21.56 sulfate –4.28 14.54 Douxan –45.69 –18.35 Triacctonamine –81.00 –75.68 Phenetylurea –46.55 –49.30 Hemedin –51.42 –57.53 Ultrasweet –45.69 –18.20 sulfate –47.05 –52.72 S 2346 –54.53 –64.21 Penbutamin –88.25 –91.74 DL 204 IT –55.05 –41.12 Guanisoquine sulfate –43.29 –39.86 Clanobulin –19.91 –25.33 nitrate –54.61 –44.54 Equilenin –79.01 –76.11 Flutonidine hydrochloride –55.98 –53.42 Vinconate –57.89 –64.51 Barbismetylii iodidum 8.92 –70.54 Diethylstilbestrol –79.86 –75.82 Vincamine methyl chloride –70.13 –76.33 Equilin –79.01 –76.17 S14 In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach J. Braz. Chem. Soc.

Table S3. Results of the classification of compounds in the test set (cont.)

Inactive compounds DP% a Inactive compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. Dipropamine –68.28 –90.44 Ethyllysergamide –56.39 –63.58 2-(2,2-Diphenylacetoxy)-N,N-diethyl- –70.34 –80.66 Hexestrol –79.86 –75.91 N-methylethanaminium –51.35 –50.71 Estrone –79.01 –76.20 Stilonium iodide –81.91 –83.94 Trenbdone –79.70 –77.38 Quateron –57.62 –64.73 Methallenestril –69.47 –76.73 Phenactropinium chloride –35.76 –47.69 Zearalenone –33.83 –30.29 Paramyon –82.31 –96.04 estrone sulfate 37.62 15.02 Benzochinoniumchlorid –18.90 –35.27 Drupanol –86.60 –84.49 Pancuronium –13.83 –50.66 Epiestriol –72.11 –67.10 Trimethidinium methosulfate –83.34 –94.84 Norclostebol –73.18 –64.22 Pentolonium tartrate –82.31 –91.30 Nandrolone –79.70 –77.55 Gaplegin –83.34 –94.84 Zeranol –37.48 –33.17 Oxamethonium iodide –77.04 –89.82 Mecysteine –50.54 –65.15 Agentit –68.02 –90.40 Tuaminoheptane –85.86 –84.60 Dimecolonium iodide –60.70 –89.83 Metexaminum –85.86 –84.52 Fubrogonium iodide –18.58 –45.48 Tyrosam –79.40 –76.66 Tetramethoquine methiodide –54.83 –83.28 ASL-7003 –68.77 –62.00 Methyloxamethonium iodide –77.60 –93.30 Amidefrini mesilas 22.24 –20.62 –84.31 –96.96 Methophedrinum –73.37 –82.95 Trepirium iodide –61.72 –90.67 Proxamine –61.67 –59.84 Imekhin –85.84 –88.07 –86.91 –88.74 Dimecamine –88.25 –91.74 Indanazoline hydrochloride –64.72 –63.46 Temechin –86.72 –84.40 –62.36 –61.01 hydrochloride –86.91 –88.90 Metizoline –68.87 –59.98 Tetramethylammonium –88.57 –95.79 –70.64 –69.92 Cyclocholine tosilate –82.36 –87.45 Tramazoline hydrochloride –64.72 –63.50 Methylene chloride –83.55 –79.53 Fenoxazoline –70.64 –69.92 Frigen 113 –20.09 –19.63 Phedrazine –51.63 –76.36 –38.31 –42.40 Clonazoline hydrochloride –71.86 –63.36 Norflurane –71.24 –73.70 Coumazoline –68.87 –59.97 Tribromethanol 21.10 –31.53 Tefazoline nitrate –78.66 –76.99 –91.19 –90.20 Tymazoline hydrochloride –70.64 –69.91 Ethyl chloride –88.95 –85.76 Isopropylmethoxamine –65.39 –77.59 –25.90 –31.76 hydrochloride –78.66 –76.99 Dioxychlorane –24.42 –24.79 hydrochloride –68.60 –65.52 –59.20 –56.90 Mtrafazoline –78.66 –76.99 –39.14 –61.89 Racefemine –81.12 –79.64 –54.68 –58.54 hydrochloride –84.99 –90.62 –91.19 –90.20 Isomylamine –72.04 –75.00 2-Chloropropane –88.54 –84.41 Cypentil –87.30 –87.36 –46.87 –52.40 –50.36 –42.48 –14.28 –32.93 –50.68 –35.23 Vinyl ether –87.56 –86.10 Dimebamate 5.78 –22.22 Vinamar –87.99 –87.38 DEP –82.41 –82.68 Isopryl –88.40 –90.58 Cresotamide –64.65 –61.81 Benzylicum –87.50 –86.46 Silamprobamate 8.69 –4.81 Metacaine –66.01 –65.95 5.78 –21.73 Subcutin –66.01 –65.89 Chlorphenesin –19.45 –21.12 Anaesthaminol –51.60 –50.48 –62.95 –69.29 Naretin –48.20 –46.28 Mephenesin –74.80 –74.63 Tireobutil –42.50 –29.96 Guaifenesin –66.66 –74.41 Vol. 26, No. 6, 2015 Castillo-Garit et al. S15

Table S3. Results of the classification of compounds in the test set (cont.)

Inactive compounds DP% a Inactive compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. –66.01 –65.89 Glyketal –73.76 –74.24 Clormecaine hydrochloride –47.46 –59.39 Flucarbril –46.82 –58.17 –66.01 –65.89 Mephenoxalone –39.45 –58.48 Isobutamben –66.01 –65.89 Mephenesin carbamate –34.05 –45.12 Basedol –59.77 –54.61 Methocarbamol –18.87 –44.72 Mercaptothiazoline –62.73 –61.83 Ebubamate 5.78 –21.34 Iodothiouracil –9.10 6.12 Strychnocarpine –68.14 –72.55 Tiouracilo –43.83 –31.89 Nafomine –83.53 –82.34 Thiamazole –58.40 –66.87 AHR-2666 –42.98 –48.20 Aminomethiazole bitartrate –58.71 –52.87 Metaxalone –52.33 –58.83 Thiamazol methyl iodide –56.09 –74.14 Luvatren –74.80 –74.61 Basthioryl –66.19 –87.04 3.28 –20.97 Mipimazole –58.71 –62.68 Pifexole –43.57 –4.81 Propyllthiouracil –42.50 –29.77 Fenyramidol hydrochloride –71.04 –63.22 Bijodtyrosin 20.72 27.26 Quiloflex –68.36 –78.16 Beta-dijodtyrosin 20.72 27.15 1.65 –25.80 Fluorotyrosinum –38.80 –34.02 Carmecolin chloride –51.41 –79.92 Fenucil –42.50 –29.14 Furtrethonium iodide –82.88 –91.75 Bentiuracil –42.50 –29.44 chloride –71.04 –87.07 Thiophenobarbital –2.25 –14.37 Dithiophos –54.31 84.02 Allantovanamide 43.14 34.57 Pyrophos –24.12 78.47 Orotric –61.68 –63.05 Tetrastigmine 11.60 71.30 Quisqua lamine –1.24 –4.17 Pyridostigmine bromide –50.53 –75.48 Isocalcio “Erba’’ –77.01 –77.45 Pilokarpin –56.59 –63.36 Treonin phosphate 18.07 45.96 Distigmine bromide 42.90 –21.16 Alloxanthine –14.09 16.44 TV 399 –71.01 –66.70 Pyrglutargine –46.06 –48.95 hydrochloride –70.67 –68.61 Mecytosine –49.68 –31.26 D 935 –71.81 –68.25 Acustasin –21.84 –27.76 Doxaminol –68.32 –75.01 Eutrit –50.73 –53.05 Oxyphenudrine –42.97 –32.96 Gaboxadol –59.57 –47.58 Benzyllephedrine –82.86 –84.69 Gluronsan –21.99 –22.02 Isalon diwag –77.45 –81.23 Esorben –30.40 –32.02 pivalate –55.55 –57.33 Didym levulinate –65.00 –65.55 SY 28 –81.12 –80.06 Fluindarol –46.09 –49.37 Pivenfrine –56.66 –65.78 Anisindione –70.88 –76.30 Methyphemin.M6T –84.53 –92.01 Omefin –69.82 –68.50 hydrochloride –82.86 –84.76 Phenprocoumon –66.45 –64.80 Varon –68.11 –84.91 2,6-Dichloro-4-nitroaniline –66.45 –64.56 hydrochloride –54.34 –76.94 Coumachlore –37.82 –25.58 –59.26 –53.75 Iowarfarin –17.50 –13.39 Detenerol hydrochloride –71.81 –68.48 Acenocoumarol 4.02 30.86 Isofenefrine –71.81 –68.54 Eticoumarolum –6.28 –6.09 hydrochloride –82.80 –89.10 Napharin –50.47 –48.81 Mephentermine –86.91 –88.74 Oxazidione –63.60 –67.13 Clorprenaline hydrochloride –74.79 –67.04 Coumetarol 6.34 –13.26 –85.86 –83.69 Clocoumarol –59.24 –51.74 –80.08 –77.94 Diphenadione –66.58 –64.78 hydrochloride –28.34 –26.01 Etiphen –66.58 –64.78 Norfefrine –70.58 –66.51 Prolame –59.49 –58.04 –70.58 –66.42 Amikhelline hydrochloride –30.63 –27.58 –57.61 –51.04 S16 In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach J. Braz. Chem. Soc.

Table S3. Results of the classification of compounds in the test set (cont.)

Inactive compounds DP% a Inactive compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. Diclofutime mesilate –32.94 –11.28 –56.35 –49.21 Stenopril –86.91 –85.87 Octodrine –85.86 –84.55 Pectol –83.50 –83.67 DIHNE –10.42 1.97 Cinepazic acid 8.70 –44.20 borate –57.85 –23.35 Efloxate –39.10 –42.34 Amfetamine –85.86 –83.93 Perflavon –64.83 –76.41 Norephedrine –79.48 –76.60 Nitrous ether –77.61 –61.03 Pulsoton –78.79 –75.14 Aminoethylnitrate –45.41 –26.85 Hydroxyamfetamine –78.79 –75.10 Clonitrate 22.41 66.08 –69.75 –64.59 Eritrityl tetranitrate 94.21 99.05 –73.36 –76.98 Pentaerythrityltetranitrate 93.77 98.84 Deoxyadrenaline –72.48 –75.98 Amyl nitrite –77.61 –61.03 –56.51 –48.50 Nitrodimethylin –42.45 –50.94 –87.30 –89.37 Nitrosorbide 42.57 72.36 Cyclopentamine –87.30 –89.37 Nitromannitol 99.79 99.99 Homorenon –57.58 –55.02 Propatyl nitrate 71.84 91.50 Phenamazoline –68.39 –66.82 Trolnitrate 78.42 93.16 sulfate –80.88 –83.01 Methylis nicotinas –70.88 –74.72 Ordenina –83.29 –88.46 Nitral 8.96 49.60 Oxyephedrine –72.59 –75.23 Ethiacin –59.24 –57.46 Etilefrine –72.59 –70.87 –2.42 24.84 Methyladrenaline –64.81 –73.70 Nitronal –61.97 –43.78 –64.85 –76.96 Ampecyclal –78.79 –76.61 para-Aminoephedrine –70.38 –72.92 Carpronium chloride –72.84 –91.24 Amezinium methylsulfate –48.26 –49.01 Dan Shen-Su –35.66 –31.03 AMT –78.01 –74.26 Nicodan percuton –69.94 –67.07 Acipimox –66.12 –66.80 6,9-Didesmethylartemisinin –43.63 –30.18 Dichlorisoprenaline –66.98 –49.17 Hydrolapachol –67.85 –64.70 hydrochloride –78.90 –74.71 Hapinone –54.01 –49.39 hydrochloride –60.75 –56.02 Atovaquone –68.85 –65.79 Benfurodil hemisuccinate 17.32 6.12 Arteflene 9.08 14.86 CV 705 –54.84 –76.82 Refigallol 27.68 41.64 Dilevalol hydrochloride –34.18 –29.72 Exifone 3.89 19.52 Pipratecol –37.22 –45.01 –58.02 –74.45 fumarate –84.47 –90.15 Dioncophyline B –60.75 –63.46 Papaverine –58.73 –82.28 Axisonitrile –84.99 –82.34 Chinotoxin –62.07 –66.11 Berbamine –8.22 –60.65 Alprostadil –35.27 –34.38 Strychnobrasiline –25.32 –37.50 Dinoprost –38.87 –36.37 Malagoshine –55.90 –69.22 Tipropidil hydrochloride –64.06 –58.66 Peroxycalamenene –83.87 –74.93 Prostaglandin F1alpha –38.87 –36.77 Hisoclinotoxin A –93.06 83.36 Apovincamine –57.89 –64.51 Cycloleucine –63.71 –63.74 Vincamine –39.80 –48.36 Nitroguanil 45.66 59.30 tartrate –73.76 –69.95 Cloguanamil 32.57 39.46 Assedil –60.93 –58.25 Cilional –63.20 –68.89 Azaclorzine hydrochloride –30.40 –5.93 Antimalarine –65.66 –69.32 Diprofenehydrochloride –69.35 –70.02 Amquinate –43.15 –48.02 hydrochloride –86.91 –85.69 Dabhekhin –74.00 –69.43 Micinicate –33.66 –30.23 Aecachinium –23.58 –39.26 –6.75 –34.14 Tebuquine –48.41 –13.91 Belarizine –76.02 –74.79 Cycloquin –29.43 –8.90 –34.09 –47.75 Vol. 26, No. 6, 2015 Castillo-Garit et al. S17

Table S3. Results of the classification of compounds in the test set (cont.)

Inactive compounds DP% a Inactive compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. Cinchonine –72.78 –62.92 –86.91 –85.76 Cinchonidine –72.78 –62.87 Odiphalin –81.04 –79.16 b- arteether –54.55 –53.34 Mecinarone –29.12 –76.82 7,7-Difluoro-b-arteether –26.54 –12.78 Depogen –52.52 –54.80 Secoartemisinim –43.63 –30.18 Iprocrololhydrochloride –5.53 –1.27 9-Epiartemisinin –43.63 –30.18 –59.46 –57.20 6-dimethyl 6-difluoromethyl- –30.32 –18.28 –48.09 –38.54 b-arteether Hexalorxylol –2.89 14.87 –18.51 –18.25 Percloroetane –2.89 14.87 Amusulalol hydrochloride 55.82 19.54 Dichorus –25.96 3.30 K 4423 –73.68 –73.50 Metriponate 11.84 27.22 hydrochloride –73.68 –73.51 Dimetrizadole –43.35 –22.05 sulfate –72.93 –72.39 Lindane –60.91 0.28 –66.32 –69.51 Actractil –69.47 –70.01 –54.84 –60.31 Bitricanate –16.01 –19.39 fumarate –56.13 –61.92 Certuna –0.01 9.28 –14.78 –25.26 Metilarecaidine –73.68 –85.18 Butocrolol –3.90 1.13 Butonate –32.95 –29.19 –48.17 –32.99 Antienite –50.46 –33.70 –43.61 –39.69 lobendazole –15.56 –23.21 hydrochloride –73.68 –73.51 Bromotimol –76.92 –72.06 –34.62 –25.33 Ascaridole –83.87 –74.93 IPS 339 –63.21 –52.47 Eucaliptol –86.66 –84.71 Chinoin 103 –73.68 –73.16 Nitramisole hydrochloride –15.87 19.28 D 2343-HCl –61.92 –66.58 Antazonite –5.54 12.71 hydrochloride –32.00 –23.24 Vincofos –24.21 18.54 ROM-203 –36.33 –44.48 Tioxidazole 2.92 –17.15 Cromipranol –61.92 –60.58 Phoxim –44.85 56.46 –1.03 –8.59 Albendazole –0.87 –11.11 –59.28 –59.06 tartrate –72.57 –70.77 Pirepolol 43.66 8.34 Crufomate –42.94 –20.33 Butyroxane –65.10 –67.13 Pexantel –73.45 –79.59 Solypertine –38.52 –53.77 Amendol –52.87 –48.07 Mindodilol –52.01 –51.68 –82.17 –82.06 –35.81 –36.82 Mezepine –82.66 –86.39 IEM-611 –68.14 –66.64 dibudinate –81.60 –84.52 hydrochloride –58.03 –51.01 hydrochloride –79.60 –86.88 Carbazeran 17.15 –3.21 hydrochloride –76.05 –75.90 Pimobendan –9.57 –6.16 –25.75 –16.49 Neo-coronaril –83.50 –83.67 Cimoxatone –53.78 –61.49 Colforsin 5.22 9.02 Fluperlapine –66.26 –69.26 Benafentrine –28.43 –59.49 Elanzepine –81.03 –82.70 hydrochloride –27.63 –78.81 –87.68 –90.10 Bufogenin –56.30 –54.34 Mariptiline hydrochloride –73.50 –65.58 Cassaine –45.61 –66.22 Pridefine hydrochloride –88.25 –87.87 Cassaidine –48.86 –67.43 hydrochloride –84.47 –90.15 43.88 52.69 Spiroxepin –67.96 –80.38 Erythrophlamine –3.25 –50.45 –86.45 –82.84 Stevaledil –40.32 –63.50 Amedalin hydrochloride –72.77 –73.67 Mioflazine hydrochloride 42.93 57.38 Ketimipramine –74.30 –81.94 Acrihellin 10.73 6.70 S18 In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach J. Braz. Chem. Soc.

Table S3. Results of the classification of compounds in the test set (cont.)

Inactive compounds DP% a Inactive compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. Almoxatone mesilate –24.95 –34.16 Ramnodigin –23.98 –26.82 Tiazesin hydrochloride –61.79 –69.01 Piperonyl butoxide –61.29 –72.38 Binedaline hydrochloride –79.37 –84.91 Cipermethrin –12.87 6.25 –79.44 –79.84 Flumethrin –8.51 21.51 hydrochloride –4.68 13.74 Cypothrin –49.20 –44.76 Prasterone –79.70 –77.32 Gossypol 20.64 32.69 Befuraline –60.59 –61.39 Tetramethrin –25.92 –34.84 Danitracen –83.36 –85.67 Phenothrin –68.61 –69.05 –82.57 –88.60 Bromopropylate –21.93 –11.83 –75.63 –58.37 Proclonol –76.22 –60.37 –87.68 –90.08 Tibenzate –76.44 –75.34 Pinafide –1.35 20.23 Thanite –42.98 –42.50 Buparvaquone –67.85 –64.65 Iodofenphos –31.38 55.25 Carnidazole 34.92 34.19 Heptenophos –46.11 –21.02 Dimetridazole –50.75 –38.78 PR-H 286 BS –25.92 –4.87 Diminazone 22.38 52.70 EN-3638 –29.94 –4.26 Homidium –46.03 –49.84 CP-17193 –43.89 –13.39 Hidroxistilbamidine –19.57 –8.56 Ovalicin –49.54 –58.33 Imidocarb 25.21 25.72 KC-8973 –81.96 –79.68 Lauroguadine 33.26 32.97 Arphamenine A 28.60 18.85 Dimidium bromide –47.31 –59.31 Dinaline –43.44 –35.63 N-methylglucamine –34.83 –49.70 Adapiprazine –65.53 –56.23 Nihidrazone –0.11 34.81 Ethydine –39.28 –40.69 Nimorazole –69.41 61.87 Orazamide –21.66 –17.42 Nithiazide 46.56 59.70 8.85 7.70 Oxophenarsine –74.42 –73.99 Tioliacic –7.03 –9.66 Parnaquone –67.85 –64.72 Tiopronin –22.28 –31.18 Quinapyramine 9.91 1.71 Nicoxamat –60.28 –48.56 Secnidazole –23.97 12.14 Citiolone –44.95 –46.42 Acranil –51.76 –33.84 Acidum metioformicum –32.32 –47.38 Stilbamine –39.73 –31.22 Methioninol –44.13 –55.62 Tinidazole 76.93 68.15 Magnesii metioglicas 59.97 55.24 Arstinol 1.49 –31.59 Ethyl glutamate –28.31 –35.98 Bialamicol –65.89 –65.09 Thioctamide –80.31 –27.06 Nitrofural 30.25 55.10 Acidum methenoxycinnamicum –55.83 –59.71 Clioquinol –50.31 –24.87 Beta-sitosterol –87.06 –85.25 Fentanilo –70.30 –68.57 Ambucetamide –57.80 –66.65 Folcodina –49.34 –62.06 Aminopromazine –69.10 –82.64 Levacetilmetadol –69.02 –75.45 Apoatropine –70.31 –74.72 Metadona –82.04 –87.59 Butaverine –71.24 –72.96 Noscapina –17.04 –59.24 N-butylscopolammonium bromide –42.65 –55.40 Oxicodona –50.42 –64.58 –38.15 –59.49 Morfina –60.61 –53.72 –82.86 –84.70 Remifentanilo 6.29 –32.07 Cyclonium iodide –73.69 –81.54 Tilidina –72.81 –83.31 Diponium bromide –69.51 –75.39 Nalorfina –63.16 –57.04 –72.04 –75.00 Bextrometorfano –84.06 –89.66 Ethaverine –53.63 –49.84 Alylprodine –71.01 –77.42 Etomiololine –43.83 –44.94 Alfentanilo 39.02 46.36 Fenalamide –38.18 –48.59 –56.56 –59.05 Fenoverine –6.40 –3.71 Benzitramine –1.38 2.87 bromide –66.69 –75.65 Vol. 26, No. 6, 2015 Castillo-Garit et al. S19

Table S3. Results of the classification of compounds in the test set (cont.)

Inactive compounds DP% a Inactive compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. Clonitazene –13.22 30.82 –55.62 –48.39 Codeinemethylbromide –65.53 –82.29 Hymecromone –66.45 –64.34 Cyclazocine –81.73 –79.33 Leiopyrrole –74.19 –71.36 Desomorphine –74.60 –76.37 Moxaverine –75.51 –81.89 Dextromoramide –65.11 –70.12 Nafiverine –27.09 –43.26 Dezocine –78.79 –75.05 Phenamacide hydrochloride –67.87 –64.44 Diampromide –71.12 –75.08 Pipoxolan hydrochloride –58.05 –61.07 aClassification of compounds by both models, equation (1) [non-Stoc.] and equation (2) [Stoc.]: DP% = [P(active) – P(inactive)] × 100; where P(active) is the probability that the equations classify a compound as active. Conversely, P(inactive) is the probability that the models classify a compound as inactive. This value (DP%) takes positive values when P(active) > P(inactive) and negative otherwise. Therefore, when DP% is positive (negative) the compound was classified as antibacterial (non-antibacterial).

Table S4. Results of the classification of compounds in the test sets

Active compounds DP% a Inactive compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. Arifen –32.88 –82.83 4-Chloro-6-cyano flavan –71.48 –59.40 Tio-urasin 70.00 54.81 PALA 78.37 76.50 Bromamphenicol 63.33 69.37 TBHQ –79.86 –76.30 Enheptin-P –21.79 24.55 Futhan 36.92 38.85 Chloramphenicol 32.63 61.76 Foscarnet –12.70 5.91 Alafosfalin 1.04 28.68 IMPY –71.75 –63.12 Zinc sulfanilate 12.40 –1.22 Aciclovir 37.44 34.96 Arsanilic acid –1.64 –76.10 SKF-23880 A –85.86 –84.44 Glucosamine hydrochloride –27.75 –29.15 Aphidicolin –63.15 –61.32 Furazonal 14.74 60.60 Moroxidine –3.29 –17.25 Nifuratrone 9.35 29.93 14.85 49.58 Solupront 91.06 80.29 Urethane –62.95 –69.89 Taurolidine 91.13 73.73 –50.93 –41.38 Thiolutin –53.86 15.35 Valerium Paul Thibault –77.01 –77.20 Arsolithol 44.40 –49.23 –72.31 –60.88 Sulfabenzamine propionate –6.31 –55.32 –86.60 –84.73 Sulfamethoxypyridazine 70.24 53.11 Methenamine –69.86 –77.43 MSD-819 63.29 58.69 Amylurea –61.65 –67.24 Chiniofon 64.61 49.33 Penthrichloral –6.15 –10.02 Nitrosulfathiazole 87.83 83.85 SOG-18 –34.53 –26.57 Nifurtoinol 61.66 76.60 –75.79 –75.92 Thiazosulfone 86.42 57.88 MECap –77.01 –77.16 Sulfamethizole 80.93 87.65 Norantoin –45.36 –56.55 Bismuthi subguajacol glycolas 96.76 92.64 Albutoin –34.55 –40.19 Sulfamonomethoxine 65.66 57.99 Cinromide –62.58 –60.58 Tetrenolin –57.40 –58.60 Fenaclon –72.27 –69.17 Broquinaldol –45.68 –24.44 Metindion –68.52 –72.98 Nifurprazine 0.23 49.54 –44.05 –55.49 Sulfacarizole 85.62 81.99 Hierro Girard –46.39 –50.97 Ferrithiocin –6.63 10.07 Fertaron –9.52 –15.96 Sulfapyrazine 52.13 56.27 Cobalti glutamas –24.61 –30.56 Sulfasomizole 51.97 54.44 Cobalti besilas –14.18 –30.13 FCE 22101 61.32 62.09 Sodium dipantoylferrate –55.97 –58.54 Aspertin –34.70 –38.03 Ferroceron –62.80 –33.95 S20 In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach J. Braz. Chem. Soc.

Table S4. Results of the classification of compounds in the test sets (cont.)

Active compounds DP% a Inactive compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. Loranil 65.48 34.53 –73.68 –85.18 Furylfuramide 4.27 33.00 Oxyphenisatin acetate –6.02 –4.02 Antibrucellim –67.85 –64.27 Bibrofenum –39.85 –23.29 Acefuralazine 46.72 78.55 Ferripyrinum –69.32 –66.99 Azidamfenicol 57.58 81.55 Hydrastine –17.04 –59.24 Pivalizid –42.62 –28.31 Polyurene 69.53 31.51 Furamizole 51.37 75.15 DS-511 –21.39 –1.58 Cinoxacin 4.69 11.63 Prorenone –65.14 –64.78 Pyrimethamine –33.50 0.82 Cicletanine –65.55 –49.48 Sulfamoyldapsone 91.62 85.84 Pamabron –79.57 –79.45 Sulfathoxypyridazin 66.57 70.16 Chlormerodrin –38.47 –68.28 Sulfamoprine 76.65 61.23 Manna sugar –34.14 –36.95 Arbutin –11.24 –7.07 Teofillina –2.67 –24.81 Bicozamycin 51.61 47.60 DS-30 –75.66 –62.26 Bromchlorofenum –18.06 20.98 Propamin “soviet” –76.84 –78.01 Pyocyanine –66.13 –64.06 WR 2823 –33.25 19.86 Salinazid –39.52 –19.22 Mexamin –75.75 –76.76 Supron 81.94 74.65 Geroquinol –79.86 –76.14 Sulfanthrolum 59.20 49.48 Ciglitazone –19.33 –26.68 Cefazaflursodium 90.89 93.33 Glisamuride 89.34 80.38 Sulfachrysoidine 87.87 87.93 MCHP –53.43 –47.90 Gliotoxin –14.52 52.26 RMI 11894 –78.03 –75.63 Metazide 22.85 40.18 Metformin –20.76 –50.53 Methyldisulfanilamide 91.33 80.51 Phenformin hydrochloride –13.57 –20.84 Amonal B –43.37 –22.91 Phenbutamide 41.96 19.47 Carbocillin 72.78 75.67 Thiazanol 63.71 54.92 Salsalate –27.53 –28.25 Clorexamide 55.20 47.69 Carbonazide –12.11 4.23 Thiohexamide 55.89 36.89 Ftivazide –24.89 –18.91 Synthalin B 9.78 –6.47 Terizidone 13.19 31.94 Bromcholine –81.06 –90.78 Sulfarsphenamine 97.38 93.03 Abbott-31699 –11.60 39.50 Dihomosulfamin 90.93 79.72 Mebetide 17.63 8.22 Penicillin S 49.83 64.29 Alarmine –80.74 –86.68 Adicillin 76.47 75.97 MJ 10459-2 –40.54 –15.03 Sulfaphenazole 54.10 57.77 Guanacline sulfate –51.42 –57.35 Cephanone 98.13 98.52 Guanoctine hydrochloride –59.65 –59.81 Sulfametoyl 41.58 29.63 Nicopholine –62.61 –60.99 96.53 97.31 Ganglefene hydrochloride –60.90 –64.20 RS 533 35.72 44.63 BAEA –63.43 –90.22 Diploicin 21.02 50.80 Pentaquinomethonium –73.95 –73.48 Rubrosal 95.92 93.84 Pentacynium chloride –63.78 –85.70 Cefetrizole 89.26 92.95 2-{5,5-diethyl-2,4,6-trimethylidene- –68.04 –78.14 3-[2-(trimethylazaniumyl)ethyl]-1,3-­­ diazinan-1-yl}ethyl)trimethylazanium 60.10 65.43 Plegarol –76.37 –86.86 98.90 99.35 Oxaditon –77.70 –92.13 Penicillin X 43.02 49.37 Dicoline –62.92 –71.87 45.35 51.49 chloride –51.41 –62.12 Baludon 99.42 98.18 Tiamethonium iodide –78.09 –92.36 Benzonaftol –77.11 –76.52 Penhexamine –88.25 –91.74 Furoxacillin 86.36 89.45 Leptodactyline –82.21 –91.23 Azoseptyl-T 84.69 87.42 Cryofluorane –26.54 –30.50 Vol. 26, No. 6, 2015 Castillo-Garit et al. S21

Table S4. Results of the classification of compounds in the test sets (cont.)

Active compounds DP% a Inactive compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. Pefloxacin –11.57 –22.82 –39.48 –51.72 Aminomethylpenicillin G 44.05 47.73 Ethyl bromide –85.71 –83.77 Ribostamycin 89.19 88.34 –25.04 –31.54 Salazo sulfapyridine 85.83 89.09 Methioflurane –50.18 –48.99 Azosulfanilamide 99.91 99.79 –67.79 –70.70 sodium 99.82 99.52 Neothyl –88.80 –91.46 77.92 75.14 Saligenol –81.17 –79.09 Isopropicillin 42.83 47.87 Novasil –52.31 –52.66 Arsutyl 98.47 95.81 –87.06 –85.49 Clindamycin 26.32 17.88 Anatiroidol –51.20 –62.39 Dibekacin 85.53 84.38 Bathyran –2.25 –16.12 73.33 86.11 Methylthiouracil –42.50 –29.86 Salazodimethoxine 95.80 94.41 Carbimazole –14.98 –35.81 -natrium 56.49 70.12 Thibenzazoline –25.54 –31.77 Epihetacillin 44.85 52.77 Diobutil –8.03 –5.35 Amantocillin 46.64 52.01 Dimaval 36.59 10.90 Streptothricin F 98.26 97.19 Imexon –43.10 –44.08 Sisomicin 78.24 71.98 Auxinutril –66.40 –71.85 Sanguinarine –44.62 –60.86 W 3580 B –74.92 –76.25 99.68 99.73 Pivalylindandione –66.58 –64.78 Latamoxefdisodium 98.01 97.74 Xylocoumarol –66.45 –64.60 Cefrotil 60.32 62.12 Dicumarol –6.28 –5.89 Picloxydine 90.16 92.58 Warfarin –50.47 –48.82 Bacmecillinam 70.57 66.10 Cyclocumarol –54.70 –64.48 T 615 –82.97 –83.67 Tioporanum 7.19 1.51 Nitrocycline 80.72 83.25 Tilsuprost 9.90 0.39 Amicycline 65.87 56.14 Visnafylline –35.68 –73.22 Sarpicillin 53.34 41.77 –56.49 –45.39 Streptomycin 99.16 98.53 Nitroglycerin 72.73 92.30 Dihydrostreptomycin 99.12 98.43 Pentrinitrol 79.65 93.62 Resistomycin –15.87 –2.48 Isosorbide mononitrate –17.33 5.92 Granaticin 59.36 63.23 Vasactin –52.89 –63.05 Metacycline 62.10 51.18 Sympatektoman-N –87.08 –88.07 Chlortetracycline 71.77 69.41 Molsidomine 28.91 25.83 Pivcefalexin hydrochloride 73.38 69.62 Berberine –48.27 –70.68 Grifolin –79.86 –76.23 Antimony sodium tioglycollate 35.16 –34.68 Habekacin 96.15 95.77 Safersan –33.77 –50.84 Surfen C 76.76 91.67 Punicine –79.47 –78.73 91.29 91.61 Iodotimol –73.43 –68.99 Minocycline 58.83 24.83 Antafenite –63.87 –57.67 Hygromycin 84.25 83.05 tartrate –72.57 –70.77 Tameticillin 57.86 37.21 Cetovex –22.30 –31.99 Arsphenamine diglucoside 88.61 89.61 Dibenzepine hydrochloride –61.77 –77.87 Alpacillin sodium 88.62 92.69 hydrochloride –78.90 –80.69 Myxothiazol 37.42 24.70 Perafensine –71.08 –68.39 Bencillin-1 56.49 70.10 hydrochloride –87.68 –90.31 Blastmycin 82.83 77.72 hydrochloride –84.42 –87.99 Tetran-amp 78.96 68.93 hydrochloride –78.37 –81.59 Rotamicillin 84.46 85.10 Prooksen –83.36 –88.60 Antimycoin 82.83 77.72 Tisocromide –33.58 14.53 Pikromycin 38.01 14.21 Perithiaden –83.94 –84.55 Pecocycline 88.21 79.82 Oxaprotine hydrochloride –82.05 –85.43 S22 In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach J. Braz. Chem. Soc.

Table S4. Results of the classification of compounds in the test sets (cont.)

Active compounds DP% a Inactive compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. Lymecycline 93.25 87.71 Ipronidazole –43.35 –22.05 Micodry 80.45 87.62 Meglumine antimoniate –34.83 –49.70 Rugulosin 62.75 69.95 Hidrocodona –65.10 –76.42 Nupheine –14.53 7.32 Narceina 22.15 –53.04 Novobiocin 91.43 86.28 Petidina –72.81 –80.34 Rosaramicin stearate 49.69 26.57 Naltrexona –44.64 –37.41 Piridicillin sodium 99.71 99.58 Amiphenazole –36.12 –26.41 Natamycin 91.58 90.27 Buprenorfina –52.29 –58.20 Neutramycin 83.72 58.17 Dimenoxadol –64.03 –79.44 Filipin 64.66 70.68 Dipipanone –80.94 –79.61 Monensin 65.89 54.06 Levallorphan –81.73 –79.31 Berythromycin 80.61 59.54 Gobad –68.36 –70.04 Penimocycline 98.97 98.89 Fenyltoloxamine –84.47 –90.15 Iprocinodine hydrochloride 99.99 99.96 Prometazine hydrochloride –74.83 –76.96 Maridomycin 96.99 91.17 –79.77 –90.53 Josamycin 92.79 80.78 Closiramine aceturate –85.16 –87.83 Megalomicin phosphate 95.65 87.27 Trastomin –84.06 –84.43 Tylosin 96.57 87.21 Perastine hydrochloride –84.06 –84.43 Septamycin 93.24 75.43 Octastine –78.06 –73.43 Etamocycline 99.67 98.75 Nibet –69.98 –86.72 Primycin 99.33 99.13 MTTA –33.33 –39.95 Efrotomycin 99.45 97.32 Chlorofibric acid –56.71 –47.29 100.00 100.00 Dipiridincarboxan –61.16 –37.47 Carumonan 99.83 99.68 Normo-level 35.87 10.46 Irloxacin –21.58 –11.95 Tiadenol –69.98 –64.87 Amifloxacin 6.35 –10.58 Nicoclonate –59.78 –45.30 Trospectomycin sulfate 32.63 6.99 Pimetine hydrochloride –85.32 –90.99 YM-13115 99.75 99.92 Nonaferone –76.32 –75.17 Fomidacillin sodium 99.15 98.97 –69.46 –65.55 Kuwanone L 73.03 81.49 Trifluomeprazine –40.98 –53.47 Aclacinomycin B 95.01 88.51 Cianothepin –62.61 –60.68 Actinomycin C3 99.99 99.95 Butropipazone –67.46 –66.20 Actinorhodine 9.61 11.95 Azabuperone –68.34 –67.45 Amidomycin 97.85 96.08 Etacepride –37.81 –51.24 7-(5-amino-5-carboxy aleramido)-3- 94.57 92.26 6,7-Dihydroxi-4-methylcoumarin 98.22 94.54 carbamoyloxymethyl-3-cephem-4- bis(hydrogen sulfate) carboxylic acid 5’’-amino-4’,5’’-dideoxyambutyrosin A 96.31 95.48 5-Bromo-2-methyl-5-nitro-1,3-dioxane –17.37 –2.44 N’-(L-gamma-amino-alpha- 99.47 99.28 N-[2,2,2-Trichloro-1-(4-morpholinyl) 0.93 –2.71 hydroxybutyryl)-Paromomycin ethyl] 6-DL-2-amino-2-(2-methyl-4-thiazolyl) 77.27 82.77 2,2,2-Trichloro-4-hydroxyacetanilide –2.30 8.83 acetamido penicillanic acid Antibiotic 810 A2 96.76 92.62 2-(4-Chlorophenoxy)ethanol –76.74 –71.23 Antibiotic A 16886 2 89.61 80.93 Dimethylsulfoxide –82.18 –80.98 Antibiotic A-30641 40.03 76.43 Antibiotic B-5050-C 96.32 89.38 3-Amino-4-hydroxybutanoic acid –52.62 –56.46 2-Propyl-5-tiazole carboxylic acid –44.83 –37.15 Antibiotic BL-S217 81.66 77.73 2-Mercapto benzotiazole –50.66 –50.18 Antibiotic BU-1975-C1 95.93 95.03 o-Acetyl-3-iodosalicylic acid –12.52 –13.30 Antibiotic cyl-2 79.41 67.62 2-Ethoxybenzamide –66.90 –66.38 Antibiotic FL-1060 11.75 20.18 2-Isopropil-4-pentenoyl urea –38.55 –46.01 Antibiotic G-418 88.72 84.88 Propanoic acid –77.01 –77.44 Antibiotic LL-AB664 96.16 92.07 Guanazole –32.62 –37.99 Antibiotic LL-BM123 alpha 99.99 99.95 Norgamem –55.21 –57.20 Vol. 26, No. 6, 2015 Castillo-Garit et al. S23

Table S4. Results of the classification of compounds in the test sets (cont.)

Active compounds DP% a Inactive compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. Antibiotic M-43365 A1 32.51 8.61 Lost –81.73 –70.80 Antibiotic MM 17880 95.21 91.93 DONU 11.03 42.17 Antibiotic P-2563 I 77.90 72.54 Xylose –49.00 –49.82 Antbiotic Ro 21-6150 85.30 77.53 Aspartame 20.97 –4.18 Antibiotic SC-30532 82.16 70.24 Dienestrol –79.86 –75.82 Antibiotic SF-733 89.19 88.34 Pipadrol hydrochloride –80.31 –78.27 Antibiotic SF-1623 99.17 98.55 Hydroxyestrone –70.04 –65.49 Antibiotic SS-228Y –13.61 –4.35 Estradiol –80.53 –77.23 Antibiotic U-20,943 38.72 40.65 Nandrolone sulfate sodium 36.00 11.90 Aplasmomycin 96.43 94.75 Solution A 40 –62.77 –61.53 Bostrycin 2.47 14.32 –78.66 –76.97 Caerulomycin –52.45 –38.25 Domazoline fumarate –71.57 –76.79 Calvatic acid 33.58 23.46 Hexatolin –26.79 –85.96 Alpha-carboxy-3-thienylmethyl 72.74 79.56 Deoxy-(0-8)-17-epi-salinomycin 59.58 63.55 penicillin B 96.76 92.64 –49.08 –55.84 Cinerubin A 97.28 96.69 Betaquil –61.80 –65.97 Coriolin –46.48 –42.21 Promoxolane –73.76 –74.17 Cariolin C –20.66 –20.74 Murexine –40.55 –70.32 Deacetylcephalosporin C 75.78 74.65 Fenyripol hydrochloride –57.52 –42.19 Deltamycin A2 96.90 90.83 3.28 –21.79 –60.64 –64.56 –71.96 –88.26 Desferritriacetylfusigenin 99.45 99.11 Ezerina –39.12 –68.28 DI-2,4-diacetylfluoroglycylmethane 64.96 71.37 3-o-Propionyl-5-o-mycaminosyl 65.19 29.21 platenolide 1 7 beta,8 beta-2’,3’-diepoxyroridin H 35.77 25.88 Lysergide –59.14 –64.86 Efrotomycin 99.41 97.02 MK-801 –86.08 –83.75 Emericid 81.49 55.84 Bamethan sulfate –72.59 –70.60 7 beta,8 beta-Epoxyroridin H 35.77 25.88 sulfate –59.26 –53.64 Erythromycin C 82.56 71.97 Dioxethedrin –59.26 –54.19 Everninomycin B 100.00 99.99 –69.63 –64.95 Fluoropolyoxin L 99.24 98.73 Pacamine –87.30 –89.45 Fomecin A –44.62 –38.93 –79.48 –76.60 Gentamicin A2 88.12 87.19 –73.36 –77.04 Gentamicin X 88.53 87.74 Ephinephrine –61.34 –65.42 Griseusin A 66.36 64.72 Metamfetamine –87.30 –89.21 Halomicin B 93.02 90.61 Dioxifedrine –60.31 –62.96 3-Hydroxypiromidic acid 28.70 43.16 Propylhexedrine –87.30 –89.37 Isororidin E 16.72 5.45 –29.81 16.62 Juvenimicin A4 47.93 24.35 Bufeniode –12.90 –0.46 Lankamycin 95.22 87.99 hydrochloride –71.01 –65.94 Lupulon –53.69 –50.75 Aligeron –83.93 –83.73 Maridomycin 4 96.37 85.80 Suloctidil –72.84 –65.00 Megalomycin C2 98.57 95.12 Alkaloid F –43.80 –54.79 Morphocycline 77.88 65.20 Cinepazide maleate 3.37 –47.68 Mycobacillin 100.00 100.00 Aceperone –46.02 –48.84 Myrtucummulone A 66.28 70.17 Ethaverine –53.63 –49.84 Nanaomycin B 9.61 11.84 PHQA 33 –61.92 –60.63 Netilmicin 65.14 58.71 hydrochloride –15.81 –18.77 Nosiheptide 100.00 100.00 hydrochloride –52.34 –55.28 Novobiocin 88.61 84.26 hydrochloride –22.59 –28.08 Penicillin BT 37.08 45.36 Nafetolol –60.75 –58.78 S24 In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach J. Braz. Chem. Soc.

Table S4. Results of the classification of compounds in the test sets (cont.)

Active compounds DP% a Inactive compounds DP% a name Non-stoc. Stoc. name Non-stoc. Stoc. Phlebiakauranol –5.00 –15.80 hydrochloride –55.97 –74.22 Vernamycin balpha 99.14 97.27 8.74 1.08 Eseridine –26.20 –52.27 –44.47 –49.46 Purpuromycin 89.08 81.17 Butopamine –59.26 –52.63 Rabelomycin –13.61 –3.94 Canfochinid –66.01 –66.63 Racenomycin C 99.62 99.27 Bufalin –54.84 –52.70 Rifamycin G 89.47 85.34 AY-17605 –32.83 –38.27 Rosamicin 49.69 26.57 –70.12 –70.33 Seldomycin factor 1 89.14 88.12 Tioctilate –76.44 –75.34 Sorbistin A2 77.90 72.71 Homocysteine thiolactone –63.85 –62.47 Spiramycin 3 95.44 80.23 Oxomethionine sodium –59.30 –63.45 Telomycin 98.98 99.14 Orotonsan S 1.70 –29.93 Toxoflavin 19.90 10.29 Succinyl-methionine 15.39 –0.78 Vermiculine 18.24 15.00 Alibendol –43.19 –56.47 Mocimycin 91.33 88.10 Bietamiverine –62.92 –67.23 Aspiculamycin 99.66 99.19 –43.40 –51.08 Beauvericin 87.34 68.86 Diisopromine –87.51 –85.65 –87.47 –92.23 Feclomine –84.40 –85.02 –41.65 –46.11 –34.24 –62.42 Octaverine –42.51 –60.21 Pinaverium –39.74 –69.91 Homoclorciclicine –79.22 –79.13 Formetamate –35.81 –65.82 hydrochloride –78.66 –77.03 aClassification of compounds by both models, equation (1) [non-Stoc.] and equation (2) [Stoc.]: DP% = [P(active) – P(inactive)] × 100; where P(active) is the probability that the equations classify a compound as active. Conversely, P(inactive) is the probability that the models classify a compound as inactive. This value (DP%) takes positive values when P(active) > P(inactive) and negative otherwise. Therefore, when DP% is positive (negative) the compound was classified as antibacterial (non-antibacterial). Vol. 26, No. 6, 2015 Castillo-Garit et al. S25

Table S5. Structure of new compounds reported in the anti-infective field with antibacterial activity S26 In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach J. Braz. Chem. Soc.

Table S5. Structure of new compounds reported in the anti-infective field with antibacterial activity (cont.) Vol. 26, No. 6, 2015 Castillo-Garit et al. S27

Table S5. Structure of new compounds reported in the anti-infective field with antibacterial activity (cont.) S28 In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach J. Braz. Chem. Soc.

Table S5. Structure of new compounds reported in the anti-infective field with antibacterial activity (cont.) Vol. 26, No. 6, 2015 Castillo-Garit et al. S29

Table S5. Structure of new compounds reported in the anti-infective field with antibacterial activity (cont.) S30 In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach J. Braz. Chem. Soc.

Table S5. Structure of new compounds reported in the anti-infective field with antibacterial activity (cont.) Vol. 26, No. 6, 2015 Castillo-Garit et al. S31

Table S5. Structure of new compounds reported in the anti-infective field with antibacterial activity (cont.) S32 In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach J. Braz. Chem. Soc.

Table S5. Structure of new compounds reported in the anti-infective field with antibacterial activity (cont.) Vol. 26, No. 6, 2015 Castillo-Garit et al. S33

Table S5. Structure of new compounds reported in the anti-infective field with antibacterial activity (cont.) S34 In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach J. Braz. Chem. Soc.

Table S5. Structure of new compounds reported in the anti-infective field with antibacterial activity (cont.) Vol. 26, No. 6, 2015 Castillo-Garit et al. S35

Table S5. Structure of new compounds reported in the anti-infective field with antibacterial activity (cont.) S36 In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach J. Braz. Chem. Soc.

Table S5. Structure of new compounds reported in the anti-infective field with antibacterial activity (cont.) Vol. 26, No. 6, 2015 Castillo-Garit et al. S37

Table S6. Results of the classification of new compounds reported in the anti-infective field with antibacterial activity

Active compoundsa DP% b Active compoundsa DP% b Name/code Non-stoc. Stoc. Name/code Non-stoc. Stoc. t 001 T-3811 34.22 36.34 t 047 85.98 73.08 t 002 WQ 3034 72.33 86.65 t 048 25.40 23.39 t 003 WQ 2724 71.96 81.73 t 049 KB 5246 33.98 31.37 t 004 WQ 2743 78.08 83.79 t 050 KB 5290 32.73 20.73 t 005 KRQ 10196 36.22 43.93 t 051 KB 6600 50.25 48.25 t 006 KRQ 10099 12.32 11.24 t 052 KB 6625 45.75 28.63 t 007 KRQ 10018 33.43 35.68 t 053 A-255916 –8.15 –11.18 t 008 KRQ 10071 33.43 34.46 t 054 A-270117 29.28 25.78 t 009 HMR 3647 94.03 87.64 t 055 77.38 71.43 t 010 TE-810 81.86 55.80 t 056 Descladinosyl 97.64 89.65 erythromycin t 011 TE-802 72.27 57.69 t 057 ABT 773 81.09 70.22 t 012 78.46 67.91 t 058 HMR 3562 95.43 90.80 t 013 88.33 81.50 t 059 HMR 3787 95.81 91.56 t 014 TEA-0769 96.28 93.05 t 060 85.21 74.94 t 015 89.14 65.15 t 061 78.55 54.58 t 016 85.72 71.10 t 062 79.86 61.30 t 017 88.89 84.91 t 063 28.72 36.31 t 018 85.72 72.03 t 064 OCA-983 72.12 69.87 t 019 85.72 72.16 t 065 96.61 90.97 t 020 PNU 101099 61.59 25.61 t 066 E-1010 46.49 51.90 t 021 PNU 101850 69.04 77.94 t 067 DK-35C 65.39 61.43 t 022 Esperezolid 29.61 18.32 t 068 26.35 29.29 t 023 MC 02479 98.73 99.31 t 069 75.24 78.79 t 024 Posaconazole 98.35 99.56 t 070 8.31 –4.92 t 025 SYN 2190 98.21 98.52 t 071 66.31 50.88 t 026 AS-924 98.43 98.03 t 072 LB 10827 99.68 99.87 t 027 74.81 77.20 t 073 MC 03971 99.91 99.94 t 028 74.81 77.47 t 074 98.86 99.11 t 029 74.81 78.35 t 075 J 110 441 18.61 36.88 t 030 74.81 77.33 t 076 95.83 90.99 t 031 PA 824 67.72 72.10 t 077 RWJ 157479 74.45 75.56 t 032 PA 1297 89.24 89.11 t 078 RWJ 153073 25.52 21.12 t 033 PGE 711699 97.16 95.91 t 079 RWJ 157498 51.87 41.62 t 034 PGE 7594630 98.11 97.44 t 080 SB 255 666 –4.57 –5.39 t 035 SCH 27 899 100.00 99.99 t 081 SB 252 619 67.70 82.99 t 036 WQ 3330 48.83 57.17 t 082 SB 264 218 44.14 33.46 t 037 WQ 2942 38.58 51.75 t 083 A 27.44 39.19 t 038 WQ 2756 62.48 76.32 t 084 C 27.44 38.91 t 039 WQ 2908 51.91 62.50 t 085 D 86.69 83.12 t 040 PGE 9262932 4.12 –6.45 t 086 PNU 172576 61.04 72.80 t 041 PGE 4175997 5.75 –4.64 t 087 PNU 171832 0.01 8.68 t 042 PGE 9509 926 4.12 –5.38 t 088 PNU 173954 –42.62 –21.81 t 043 NFSQ 88.71 86.66 t 089 –20.03 –8.57 t 044 87.41 80.22 t 090 INF 55 –46.18 –53.61 t 045 93.98 95.38 t 091 INF 277 –48.61 –37.89 t 046 81.47 76.99 t 092 INF 241 –64.81 –61.73 t 093 INF 392 –8.63 –14.43 t 105 –27.96 8.58 t 094 INF 271 –48.67 –58.34 t 106 SEP 137199 –42.08 –22.25 t 095 MC 207 110 53.13 46.97 t 107 SEP 32196 25.37 39.37 t 096 UK 57 562-01 35.66 12.21 t 108 SEP 132617 25.37 34.96 t 097 CHIR 29498 36.49 25.21 t 109 SB-268091 –25.14 –20.54 S38 In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach J. Braz. Chem. Soc.

Table S6. Results of the classification of new compounds reported in the anti-infective field with antibacterial activity (cont.)

Active compoundsa DP% b Active compoundsa DP% b Name/code Non-stoc. Stoc. Name/code Non-stoc. Stoc. t 098 Bis benzilamide eromomycin 100.00 100.00 t 110 SB-247386 14.91 3.15 t 099 Vancomycin –61.40 –69.88 t 111 KY-9 19.24 29.91 t 100 –51.26 –51.42 t 112 Ro 62-6091 45.94 44.53 t 101 –63.91 –72.58 t 113 Ro 64-5781 56.37 67.02 t 102 –52.45 –52.63 t 114 VRC 483 28.82 27.22 t 103 Psammaplin A 82.04 97.63 t 115 9567 567 97.89 95.86 t 104 HKI 97 24037 99.99 99.97 t 116 5522 293 98.52 97.17 aChemicals 1-33 and 34-87 were taken from references 1 and 2, respectively. The molecular structures of these compounds are illustrated in Table SM5; bclassification of compounds by both models, equation (1) [non-Stoc.] and equation (2) [Stoc.]: DP% = [P(active) – P(inactive)] × 100.

References

1. Bryskier, A. Clin. Infect. Dis. 1998, 27, 865. 2. Bryskier, A. Clin. Infect. Dis. 2000, 31, 1423.